Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.
Any method used for determining the location of and relative distances between genes on a chromosome.
Chromosomes in which fragments of exogenous DNA ranging in length up to several hundred kilobase pairs have been cloned into yeast through ligation to vector sequences. These artificial chromosomes are used extensively in molecular biology for the construction of comprehensive genomic libraries of higher organisms.
Short tracts of DNA sequence that are used as landmarks in GENOME mapping. In most instances, 200 to 500 base pairs of sequence define a Sequence Tagged Site (STS) that is operationally unique in the human genome (i.e., can be specifically detected by the polymerase chain reaction in the presence of all other genomic sequences). The overwhelming advantage of STSs over mapping landmarks defined in other ways is that the means of testing for the presence of a particular STS can be completely described as information in a database.
Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)
A technique with which an unknown region of a chromosome can be explored. It is generally used to isolate a locus of interest for which no probe is available but that is known to be linked to a gene which has been identified and cloned. A fragment containing a known gene is selected and used as a probe to identify other overlapping fragments which contain the same gene. The nucleotide sequences of these fragments can then be characterized. This process continues for the length of the chromosome.
DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.
A species of temperate bacteriophage in the genus P1-like viruses, family MYOVIRIDAE, which infects E. coli. It is the largest of the COLIPHAGES and consists of double-stranded DNA, terminally redundant, and circularly permuted.
Plasmids containing at least one cos (cohesive-end site) of PHAGE LAMBDA. They are used as cloning vehicles.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
A method for ordering genetic loci along CHROMOSOMES. The method involves fusing irradiated donor cells with host cells from another species. Following cell fusion, fragments of DNA from the irradiated cells become integrated into the chromosomes of the host cells. Molecular probing of DNA obtained from the fused cells is used to determine if two or more genetic loci are located within the same fragment of donor cell DNA.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).
The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.
Analysis of PEPTIDES that are generated from the digestion or fragmentation of a protein or mixture of PROTEINS, by ELECTROPHORESIS; CHROMATOGRAPHY; or MASS SPECTROMETRY. The resulting peptide fingerprints are analyzed for a variety of purposes including the identification of the proteins in a sample, GENETIC POLYMORPHISMS, patterns of gene expression, and patterns diagnostic for diseases.
Methods used for studying the interactions of antibodies with specific regions of protein antigens. Important applications of epitope mapping are found within the area of immunochemistry.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
The genetic complement of a plant (PLANTS) as represented in its DNA.
Imaging techniques used to colocalize sites of brain functions or physiological activity with brain structures.
Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.
A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.
Recording of regional electrophysiological information by analysis of surface potentials to give a complete picture of the effects of the currents from the heart on the body surface. It has been applied to the diagnosis of old inferior myocardial infarction, localization of the bypass pathway in Wolff-Parkinson-White syndrome, recognition of ventricular hypertrophy, estimation of the size of a myocardial infarct, and the effects of different interventions designed to reduce infarct size. The limiting factor at present is the complexity of the recording and analysis, which requires 100 or more electrodes, sophisticated instrumentation, and dedicated personnel. (Braunwald, Heart Disease, 4th ed)
Sequential operating programs and data which instruct the functioning of a digital computer.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).
Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.
A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.
Deoxyribonucleic acid that makes up the genetic material of plants.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
Recording the locations and measurements of electrical activity in the EPICARDIUM by placing electrodes on the surface of the heart to analyze the patterns of activation and to locate arrhythmogenic sites.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.
A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.
The systematic study of the complete DNA sequences (GENOME) of organisms.
A specific pair of human chromosomes in group A (CHROMOSOMES, HUMAN, 1-3) of the human chromosome classification.
The functional hereditary units of PLANTS.
The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.
A specific pair of GROUP E CHROMOSOMES of the human chromosome classification.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.
The genetic complement of a BACTERIA as represented in its DNA.
Any cell, other than a ZYGOTE, that contains elements (such as NUCLEI and CYTOPLASM) from two or more different cells, usually produced by artificial CELL FUSION.
A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.

A sequence-ready BAC clone contig of a 2.2-Mb segment of human chromosome 1q24. (1/676)

Human chromosomal region 1q24 encodes two cloned disease genes and lies within large genetic inclusion intervals for several disease genes that have yet to be identified. We have constructed a single bacterial artificial chromosome (BAC) clone contig that spans over 2 Mb of 1q24 and consists of 78 clones connected by 100 STSs. The average density of mapped STSs is one of the highest described for a multimegabase region of the human genome. The contig was efficiently constructed by generating STSs from clone ends, followed by library walking. Distance information was added by determining the insert sizes of all clones, and expressed sequence tags (ESTs) and genes were incorporated to create a partial transcript map of the region, providing candidate genes for local disease loci. The gene order and content of the region provide insight into ancient duplication events that have occurred on proximal 1q. The stage is now set for further elucidation of this interesting region through large-scale sequencing.  (+info)

Pleiotropic skeletal and ocular phenotypes of the mouse mutation congenital hydrocephalus (ch/Mf1) arise from a winged helix/forkhead transcriptionfactor gene. (2/676)

Congenital hydrocephalus is an etiologically diverse, poorly understood, but relatively common birth defect. Most human cases are sporadic with familial forms showing considerable phenotypic and etiologic heterogeneity. We have studied the autosomal recessive mouse mutation congenital hydrocephalus ( ch ) to identify candidate human hydrocephalus genes and their modifiers. ch mice have a congenital, lethal hydrocephalus in association with multiple developmental defects, notably skeletal defects, in tissues derived from the cephalic neural crest. We utilized positional cloning methods to map ch in the vicinity of D13Mit294 and confirm that the ch phenotype is caused by homozygosity for a nonsense mutation in a gene encoding a winged helix/forkhead transcription factor ( Mf1 ). Based on linked genetic markers, we performed detailed phenotypic characterization of mutant homozygotes and heterozygotes to demonstrate the pleiotropic effects of the mutant gene. Surprisingly, ch heterozygotes have the glaucoma-related distinct phenotype of multiple anterior segment defects resembling Axenfeld-Rieger anomaly. We also localized a second member of this gene family ( Hfh1 ), a candidate for other developmental defects, approximately 470 kb proximal to Mf1.  (+info)

Evidence for an ancient chromosomal duplication in Arabidopsis thaliana by sequencing and analyzing a 400-kb contig at the APETALA2 locus on chromosome 4. (3/676)

As part of the European Scientists Sequencing Arabidopsis program, a contiguous region (396607 bp) located on chromosome 4 around the APETALA2 gene was sequenced. Analysis of the sequence and comparison to public databases predicts 103 genes in this area, which represents a gene density of one gene per 3.85 kb. Almost half of the genes show no significant homology to known database entries. In addition, the first 45 kb of the contig, which covers 11 genes, is similar to a region on chromosome 2, as far as coding sequences are concerned. This observation indicates that ancient duplications of large pieces of DNA have occurred in Arabidopsis.  (+info)

A contiguous 3-Mb sequence-ready map in the S3-MX region on 21q22.2 based on high- throughput nonisotopic library screenings. (4/676)

Progress in complete genomic sequencing of human chromosome 21 relies on the construction of high-quality bacterial clone maps spanning large chromosomal regions. To achieve this goal, we have applied a strategy based on nonradioactive hybridizations to contig building. A contiguous sequence-ready map was constructed in the Down syndrome congenital heart disease (DS-CHD) region in 21q22.2, as a framework for large-scale genomic sequencing and positional candidate gene approach. Contig assembly was performed essentially by high throughput nonisotopic screenings of genomic libraries, prior to clone validation by (1) restriction digest fingerprinting, (2) STS analysis, (3) Southern hybridizations, and (4) FISH analysis. The contig contains a total of 50 STSs, of which 13 were newly isolated. A minimum tiling path (MTP) was subsequently defined that consists of 20 PACs, 2 BACs, and 5 cosmids covering 3 Mb between D21S3 and MX1. Gene distribution in the region includes 9 known genes (c21-LRP, WRB, SH3BGR, HMG14, PCP4, DSCAM, MX2, MX1, and TMPRSS2) and 14 new additional gene signatures consisting of cDNA selection products and ESTs. Forthcoming genomic sequence information will unravel the structural organization of potential candidate genes involved in specific features of Down syndrome pathogenesis.  (+info)

Expressed sequence tags from immature female sexual organ of a liverwort, Marchantia polymorpha. (5/676)

A total of 970 expressed sequence tag (EST) clones were generated from immature female sexual organ of a liverwort, Marchantia polymorpha. The 376 ESTs resulted in 123 redundant groups, thus the total number of unique sequences in the EST set was 717. Database search by BLAST algorithm showed that 302 of the unique sequences shared significant similarities to known nucleotide or amino acid sequences. Six unique sequences showed significant similarities to genes that are involved in flower development and sexual reproduction, such as cynarase, fimbriata-associated protein and S-receptor kinase genes. The remaining unique 415 sequences have no significant similarity with any database-registered genes or proteins. The redundant 123 ESTs implied the presence of gene families and abundant transcripts of unknown identity. Analyses of the coding sequences of 61 unique sequences, which contained no ambiguous bases in the predicted coding regions, highly homologous to known sequences at the amino acid level with a similarity score greater than 400, and with stop codons at similar positions as their possible orthologues, indicated the presence of biased codon usage and higher GC content within the coding sequences (50.4%) than that within 3' flanking sequences (41.9%).  (+info)

Refinement of the RP17 locus for autosomal dominant retinitis pigmentosa, construction of a YAC contig and investigation of the candidate gene retinal fascin. (6/676)

The RP17 locus for autosomal dominant retinitis pigmentosa has previously been mapped to chromosome 17q by linkage analysis. Two unrelated South African families are linked to this locus and the identification of key recombination events assigned the RP17 locus to a 10 cM interval on 17q22. The work reported here refines the mapping of the locus from a 10 cM to a 1 cM interval between the microsatellite markers D17S1604 and D17S948. A physical map of this interval was constructed using information from the Whitehead/MIT YAC contig WC 17.8. Sequence-tagged site (STS) content mapping of seven overlapping YACs from this contig was employed in order to build the map. A BAC library was screened to cover a gap in the YAC contig and two positive BACs were identified. Intragenic polymorphisms in the retinal fascin gene provided evidence for the exclusion of this candidate as the RP17 disease gene.  (+info)

Revealing hidden interval graph structure in STS-content data. (7/676)

MOTIVATION: STS-content data for genomic mapping contain numerous errors and anomalies resulting in cross-links among distant regions of the genome. Identification of contigs within the data is an important and difficult problem. RESULTS: This paper introduces a graph algorithm which creates a simplified view of STS-content data. The shape of the resulting structure graph provides a quality check - coherent data produce a straight line, while anomalous data produce branches and loops. In the latter case, it is sometimes possible to disentangle the various paths into subsets of the data covering contiguous regions of the genome, i.e. contigs. These straight subgraphs can then be analyzed in standard ways to construct a physical map. A theoretical basis for the method is presented along with examples of its application to current STS data from human genome centers. AVAILABILITY: Freely available on request.  (+info)

Comparative mapping of the region of human chromosome 7 deleted in williams syndrome. (8/676)

Williams syndrome (WS) is a complex developmental disorder resulting from the deletion of a large (approximately 1.5-2 Mb) segment of human chromosome 7q11.23. Physical mapping studies have revealed that this deleted region, which contains a number of known genes, is flanked by several large, nearly identical blocks of DNA. The presence of such highly related DNA segments in close physical proximity to one another has hampered efforts to elucidate the precise long-range organization of this segment of chromosome 7. To gain insight about the structure and evolutionary origins of this important and complex genomic region, we have constructed a fully contiguous bacterial artificial chromosome (BAC) and P1-derived artificial chromosome (PAC) contig map encompassing the corresponding region on mouse chromosome 5. In contrast to the difficulties encountered in constructing a clone-based physical map of the human WS region, the BAC/PAC-based map of the mouse WS region was straightforward to construct, with no evidence of large duplicated segments, such as those encountered in the human WS region. To confirm this difference, representative human and mouse BACs were used as probes for performing fluorescence in situ hybridization (FISH) to metaphase and interphase chromosomes. Human BACs derived from the nonunique portion of the WS region hybridized to multiple, closely spaced regions on human chromosome 7q11.23. In contrast, corresponding mouse BACs hybridized to a single site on mouse chromosome 5. Furthermore, FISH analysis revealed the presence of duplicated segments within the WS region of various nonhuman primates (chimpanzee, gorilla, orangutan, and gibbon). Hybridization was also noted at the genomic locations corresponding to human chromosome 7p22 and 7q22 in human, chimpanzee, and gorilla, but not in the other animal species examined. Together, these results indicate that the WS region is associated with large, duplicated blocks of DNA on human chromosome 7q11.23 as well as the corresponding genomic regions of other nonhuman primates. However, such duplications are not present in the mouse.  (+info)

We obtained 377,980,276 raw reads (i.e., 300 bp sequences from random points in the genome), containing a total of 113.394 Gbp of sequence, or approximately 40X coverage of the tule elk genome. More than 98% of these data passed quality filtering. The reads (and coverage) were distributed approximately equally among the 4 elk, resulting in approximately 10X coverage for each of the 4 elk.. .... The tule elk reads were de novo assembled into 602,862 contiguous sequences (contigs) averaging 3,973 bp in length (N50 = 6,885 bp, maximum contig length = 72,391 bp), for a total genome sequence size of 2.395 billion bp (Gbp). All scaffolds and raw reads will be made publicly available on Genbank or a similar public database pending publication. Alignment of all elk reads back to these contigs revealed 3,571,069 polymorphic sites (0.15% of sites). Assuming a similar ratio of heterozygous (in individuals) to polymorphic (among the 4 elk) sites as we observed in the subsample aligned to the sheep genome, ...
Assembler Tasm. Download32 is source for assembler tasm shareware, freeware download - Advanced Assembler , PopAsm, the Popular Assembler , asmx , MiniDV Assembler 0.96 , Flat Assembler for Linux, etc.
DNA BASER Assembler - affordable sequence assembly, free and safe download. DNA BASER Assembler - affordable sequence assembly latest version: Tool used to assemble DNA samples.
The eRP arrangement strategy enable large-scale contig arrangement that allows for an observation of the genomic structure using the replication behavior that is common to all living things without requiring sequence information. The base composition bias, skewed oligomers, and gene directions are representative of biological information that is related to the genomic structure. However, in the case of de novo genome sequencing, there are not many cases in which the gene direction or replication origin and terminus are clearly annotated. This strategy overcomes these limitations by employing replication behavior in the genome assembly.. The use of biological information in genome assembly or scaffolding has become more common since the introduction of GFinisher, a tool that use the base compositional bias called GC skew [34]. In this study, we utilized the intracellular replication behavior as new biological information. Our research revealed that the replication behavior could clearly be ...
Since I am incredibly stupid when it comes to computers, i thought assembler was a programming language like C or C++ and could run on any machine. Only recently did I discover that the Assembler language changes by which computer you are using it, so that it is much harder for comptuers to trade programs and source code with each other. This brings me to viruss, which I have read to be sometimes written in assembler. My question is, how does a program written in a particular version of a
Finds sub-sequences or patterns in the sequence and highlights the matching regions. The tool works with standard single letter nucleotide or protein codes including ambiguities and can match Prosite patterns in protein sequences. More... ...
Finds sub-sequences or patterns in the sequence and highlights the matching regions. The tool works with standard single letter nucleotide or protein codes including ambiguities and can match Prosite patterns in protein sequences. More... ...
Distribution of contigs by size of longest ORF. Solid line, contigs with any database homology by BLASTX (1,445). Dotted line, contigs without database homology
Design of 454 pyrosequencing contig generated from the digestion of genomic DNA with restriction enzymes (EcoRI and BspEI), the addition of restriction site spe
This file presents validation information showing the degree of corroboration of clone mappings in the fingerprint map and sequence. For each clone in the rearray, a 10-clone neighbourhood is selected from neighbouring canonical map clones with sequence coordinates. The union of sequence coordinates of these map clones from a set of neighbourhoods against which the clones sequence position is compared.. The last field in this file reports the level of corroboration: inside indicates that the clones sequence mapping is within its map-derived neighbourhood, outside indicates that the clones position is on a different chromosome than suggested by its map-derived neighbourhood, NUM when the field is a number the clone is on the same chromosome as the neighbourhood, but not overlapping, and the number is the distance between the two positions, none indicates that the clone had no coordinate-bearing neighbours.. ...
Molecular Cloning, also known as Maniatis, has served as the foundation of technical expertise in labs worldwide for 30 years. No other manual has been so popular, or so influential.
bdv sorry. It is for option 1. The mapping of contigs to a reference using BLAT (BLAT/BLAST section). From BLAT generate the syntenylist (baiscally the orientation layout of contigs) which you can use subsequently to Join (you find it in the Artemis/MUMmer section) in an artificial chromosome using spacers and/or linker providing an EMBL layout file as well for inspecting in for instance ACT or Artemis of Sanger.. ...
Results : About 50% of the mRNA-sequencing reads in BME were non-bovine; after contig assembly, up to two thirds of the non-bovine reads mapped to microbial mRNAs (Fig. 1B). IRDye-capB mRNA accumulated in murine intestinal mucosa and liver (and perhaps brain) 6 h and 24 h, respectively, after oral gavage (Fig. 2). Microbial mRNAs, including 55 and 36 mRNAs from P. fluorescens and E. coli were detected in human plasma after but not before a milk meal (Tables 1, 2). capB mRNA-loaded liposomes activated NF-kB and IFN signaling in reporter macrophages (Fig. 3A). C57BL/6 mice fed a BME-depleted diet died within 11 days of influenza A challenge whereas controls fed a BME-sufficient diet survived (Fig. 3B).. ...
Ultimately, there is a relatively small limit on the size of a fragment (generally well under a kilobase, though I think Ive seen discussion on SEQAnswers of kilobase+ fragments in Illumina) which can function in the systems, so to go longer mate-pair approaches were developed. These generate two reads known to be separated by a relatively long distance, on the scale of kilobases. These solve the problem by a bunch of trickery eliminating the intervening DNA but retaining linked tags. Such schemes typically involve shearing, ligation (or in vitro recombination) into circles, another shearing step, capture of the junction fragments and conversion into a library. A bunch of work, and with a number of serious disadvantages. In particular, they tend to require tremendous amounts of upfront DNA, often tens of micrograms. The length of the original inserts are limited by what can be efficiently circularized. Most mate pair approaches shoot for under 20Kb, though Lucigen has a clever kit aimed to ...
UT Austins iGEM team developed a kit to address genetic part incompatibility in non-model organisms, and they used Benchling to make this work possible.
Both ABYSS and KAligner are run only once per assembly, which speeds up the paired-end assembly stage by nearly a factor of two. The k-mer coverage information is correct in every contig file. A tool is included to convert colour-space contigs to nucleotide contigs. Discard reads that fail the chastity filter.
in every other version of the GNU assembler i have used I can pass a string terminated with either chars or chars to a macro.
Scaffold. The route through the graph is not clear but evidence from paired data supports the connection of two contigs. A single contig is then reported with N characters between the two connected regions. This entity is also known as a scaffold. The number of N characters represents the expected distance between the regions, based on the evidence the paired data. ...
As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC library. These BAC clones provide approximately 13-fold redundant coverage of the genome and have been assembled into 376 fingerprint contigs. A yeast artificial chromosome (YAC) map was also constructed and aligned with the BAC map via fingerprinted BAC and P1 artificial chromosome clones (PACs) sharing interspersed repetitive sequence markers with the YAC-based physical map. We have annotated 95% of the fingerprint map clones in contigs with coordinates on the version 3.1 rat genome sequence assembly, using BAC-end sequences and in silico mapping methods. These coordinates have allowed anchoring 358 of the 376 fingerprint map contigs onto the sequence assembly. Of these, 324 contigs are anchored to rat genome sequences localized to chromosomes, and 34 contigs are anchored to unlocalized portions of the ...
To align the developing chicken BAC contig physical maps with the existing linkage map, its necessary to identify BACs corresponding to the DNA-based markers on the latter. Chicken BAC libraries, derived from DNA of a single UCD001 inbred Red Jungle Fowl, have been generated by our collaborators. Characterization of the first BAC library based on BamHI partial digest fragments initially was done by filter hybridization with pools of labeled, PCR-amplified fragments based on marker or gene DNA sequences. Individual marker/BAC assignments were made by Southern hybridization of BAC DNA with individual marker probes and/or PCR analysis. In this manner, 31 markers from 9 linkage groups generated 71 BamHI BAC candidates (2.3 clones per locus). This approach is labor- and cost-intensive. Thus, we began using pools of overgo probes, that are complementary synthetic oligonucleotides extended in vitro to generate ~40 base pair, double-stranded DNA probes. Two BAC libraries were hybridized to pools of 36 ...
Anchored physical maps represent essential frameworks for map-based cloning, comparative genomics studies, and genome sequencing projects. High throughput anchoring can be achieved by polymerase chain reaction (PCR) screening of bacterial artificial chromosome (BAC) library pools with molecular markers. However, for large genomes such as wheat, the development of high dimension pools and the number of reactions that need to be performed can be extremely large making the screening laborious and costly. To improve the cost efficiency of anchoring in such large genomes, we have developed a new software named Elephant (electronic physical map anchoring tool) that combines BAC contig information generated by FingerPrinted Contig with results of BAC library pools screening to identify BAC addresses with a minimal amount of PCR reactions. Elephant was evaluated during the construction of a physical map of chromosome 3B of hexaploid wheat. Results show that a one dimensional pool screening can be sufficient to
STARS is an alternative interface to staden for sequence assembly for sequence typing projects. Sequence typing projects typically involve the sequencing of the same gene, or gene fragment, many times in order to determine polymorphisms. The standard staden interfaces, pregap4 and gap4,are more suited to assembling long contigs. The STARS interface, on the other hand has been designed with sequence typing projects in mind and allows the assembly of large numbers of short contigs into the same database. These contigs can be retrieved and edited from the interface using a standard staden contig editor. The system also performs user logging etc and can therefore be used as a lab database for your projects. The software was initially designed for managing sequencing projects using Multi Locus Sequence Typing (MLST) of bacteria. It is available free of charge under the General Public License. This software is for UNIX systems and you will first need to install Staden. STARS is written by Man-Suen ...
Using high-resolution genetic mapping techniques, we have restricted the position of the Lps gene to a 0.9-cM region of chromosome 4, flanked proximally by D4Nds9 and distally by D4Mit178. A 1.7-Mb cloned DNA contig spanning this interval was sequentially assembled using YAC, BAC, and P1 clones. Our data differ significantly from another recently published physical map encompassing the Lps locus ((37)). In this contig, a gap (estimated at 100 kb by fluorescence in situ hybridization) exists in the BAC contig between D4Nds9 and D4Mit178. Comparison of BAC clone addresses common to both maps suggests that this gap corresponds to the center of our contig, and is ∼950 kb in size. Finally, through cDNA selection and nucleotide sequencing of randomly cloned sheared BACs from our contig, we have identified three transcription units within the Lps candidate region, including Tlr4, and two novel genes.. We provide evidence that implicates mouse Tlr4 as a critical regulator of the innate host response ...
Assembling a large genome using next generation sequencing reads requires large computer memory and a long execution time. To reduce these requirements, we propose an extension-based assembler, called JR-Assembler, where J and R stand for jumping extension and read remapping. First, it uses the read count to select good quality reads as seeds. Second, it extends each seed by a whole-read extension process, which expedites the extension process and can jump over short repeats. Third, it uses a dynamic back trimming process to avoid extension termination due to sequencing errors. Fourth, it remaps reads to each assembled sequence, and if an assembly error occurs by the presence of a repeat, it breaks the contig at the repeat boundaries. Fifth, it applies a less stringent extension criterion to connect low-coverage regions. Finally, it merges contigs by unused reads. An extensive comparison of JR-Assembler with current assemblers using datasets from small, medium, and large genomes shows that JR
Computer scientists at UC San Diego and Saint Petersburg State University have developed a new approach to genome assembly that will help scientists identify new viruses in complex samples. The technique, called metaviralSPAdes, allows researchers and clinicians to delineate a single viral genome, even when it is mixed with thousands of others viruses and bacteria. The study was recently published in the journal Bioinformatics.. When a new virus emerges, biologists rush to reconstruct its genome, a prerequisite for future diagnostics and vaccine development, said Pavel Pevzner, Ronald R. Taylor Professor of Computer Science in the Computer Science and Engineering Department at UC San Diego and senior author on the paper. The challenge with viral sequencing is that a sample from a patient, like the saliva from the COVID-19 patient used to assemble the first SARS-COV-2 genome, contains genomes from many other viruses. There may also be hundreds, or even thousands, of bacterial genomes. This ...
We have built a robust rice physical map. More than 65,000 BAC clones representing 20-fold coverage have been fingerprinted successfully and assembled into physical contigs. The integrity of the contig assembly and clone order has been confirmed independently by FPC Simulated Digest using sequenced BAC and PAC clones from GenBank. Approximately 90% of the rice genome has been anchored genetically. Among the genetically anchored contigs, ∼80% are anchored by two or more genetic markers and therefore are oriented properly, whereas ,80% are anchored by multiple methods (i.e., marker hybridization, in silico hybridization, FISH, and sequenced clones).. On the basis of the physical map, we estimated the euchromatic portion of the rice genome to be ∼400 Mb, whereas earlier studies estimated the rice genome to be 430 Mb, based on DNA content (Arumuganathan and Earle, 1991; Saji et al., 2001). In contrast to the previous estimate of 51.5 Mb for chromosome 1 (Table 1) (Saji et al., 2001), our size ...
Shotgun sequencing is the most widely used technique for determining the DNA sequence of organisms. It involves breaking up the DNA into many small pieces that can be read by automated sequencing machines, then piecing together the original genome using specialized software programs called assemblers. Due to the large amounts of data being generated and to the complex structure of most organisms genomes, successful assembly programs rely on sophisticated algorithms based on knowledge from such diverse fields as statistics, graph theory, computer science, and computer engineering. Throughout this chapter we will describe the main computational challenges imposed by the shotgun sequencing method, and survey the most widely used assembly algorithms.
agp-version 2.0 # ORGANISM: Homo sapiens # TAX_ID: 9606 # ASSEMBLY NAME: EG1 # ASSEMBLY DATE: 09-November-2011 # GENOME CENTER: NCBI # DESCRIPTION: Example AGP specifying the assembly of chromosome Y from WGS scaffolds # COMMENTS: # Three scaffolds are placed but have unknown orientation. chrY 1 10000 1 N 10000 telomere no na chrY 10001 13043 2 W EG1_scaffold1 1 3043 ? chrY 13044 63043 3 N 50000 contig no na chrY 63044 3434094 4 W EG1_scaffold2 1 3371051 + chrY 3434095 3484094 5 N 50000 contig no na chrY 3484095 3576421 6 W EG1_scaffold3 1 92327 + chrY 3576422 3626421 7 N 50000 contig no na chrY 3626422 3633571 8 W EG1_scaffold4 1 7150 + chrY 3633572 3683571 9 N 50000 contig no na chrY 3683572 3689149 10 W EG1_scaffold5 1 5578 + chrY 3689150 3739149 11 N 50000 contig no na chrY 3739150 3817095 12 W EG1_scaffold6 1 77946 + chrY 3817096 3867095 13 N 50000 contig no na chrY 3867096 5466918 14 W EG1_scaffold7 1 1599823 + chrY 5466919 5516918 15 N 50000 contig no na chrY 5516919 6945193 16 W ...
Genomic sequence contigs for unfinished chromosomes are assembled and laid out based largely on the clone tiling path. However, the tiling paths do not specify the orientation of the clone sequences or how they should be joined; therefore, data on the alignment of the input genomic sequences to each other and to other sequences are also used to guide the assembly. Genomic sequences that augment the initial set of genomic contigs based on the tiling path clones are also incorporated ...
ul,,li,Preparation of EST data: Sequences were extracted from dbEST and were subjected to quality control screening (vector, E. coli, polyA, T, or CT removal, minimum length = 100 bp, < 3% N).,/li,,li,Preparation of transcript (ET) database: All sequences from the appropriate divisions of GenBank (including RefSeq) were extracted. Non-coding sequences were discarded and cDNAs and coding sequences from genomic entries were saved. Sequences and related information (e.g. PubMed links) are stored in the qcGene database (qcGene).,/li,,li,Assembly: Cleaned EST sequences and non-redundant transcript (ET) sequences were combined. Using the Paracel Transcript Assembler Program, sequences were assembled into contigs. TCs are consensus sequences based on two or more ESTs (and possibly an ET) that overlap for at least 40 bases with at least 94% sequence identity. These strict criteria help minimize the creation of chimeric contigs. These contigs are assigned a TC (Tentative Consensus) number. TCs may ...
mothur , rename.file(count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count_table, tree=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.phylip.tre, shared=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.shared, constaxonomy=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.0.03.cons.taxonomy) Current files saved by mothur: accnos=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.accnos column=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.dist fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta group=stability.contigs.good.groups list=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.pick.tx.list name=stability.trim.contigs.good.names ...
I download tool QUAST and there I can see metric N50, L50, where is easy to develop own computation. But how I can measure error rate of my output contigs? Is there any tool which can do it? I searched in many papers but I cannot find way how they do it. I would like to compare with some assemblers with some general way. I found only hints that it should be done by aligning contigs to reference genomes but I do not know how and if it is right way.. ...
This Contig Editor Commands menu function operates in a very similar manner to the main Gap4 List Confidence command (see section List Confidence), except that it only operates on the current contig, and it uses the current editor consensus confidences rather than the ones saved to disk. It displays a dialogue requesting a range within the contig and a question asking if only summary of the results is required. Pressing OK or Apply will add to the editor information line a count of the expected number of errors and the error rate. If the Only update information line question was answered No then the full frequency table will also be output. It will appear in the main text output window in the same format as the List Confidence command in the main Gap4 View menu. The Apply button can be used to calculate the number of errors without removing the dialogue. It is often the very ends of contigs (which are generally low coverage and bad quality) that have most of the errors, and so it is ...
There are a number of mappers available in Geneious. Some mappers are not bundled with Geneious but may be installed as optional plugins...
Easy 1-Click Apply (STAFFMARK) Process Assembler job in Honea Path, SC. View job description, responsibilities and qualifications. See if you qualify!
SCORE============================================Contig004682============================================ 660 ============================================Contig013845============================================1162 57 --------------------------------------------------------------------------------,JMFF051H21 ,----------------------------------------rJMFF051H21 68 -----------------------------------------------------------------------------------------------,JMFF044I04 ,----------------------------------------------------rJMFF044I04 72 ---------------------------------------------------------------------,JMFF037P06 ,-----------------------------------------------------------------rJMFF037P06 81 ------------------------------------------------------------------------------------------,JMFF025B05 ,-----------------------------------------------------------------rJMFF025B05 110 -----------------------------------------------------------------------------,JMFF028E21 ...
SCORE============================================Contig000140============================================ 668 ============================================Contig002535============================================ 810 2 -----------------------------------------------------------------------------------,JMFF026E19 ,----------------------------------------------------------------------------------------------rJMFF026E19 2 --------------------------------------------------------------------------------------------,JMFF035C08 ,----------------------------------------------------------------------------------------------rJMFF035C08 4 -----------------------------------------------------------------------------------------,JMFF009N06 ,----------------------------------------------------------------------------------------------rJMFF009N06 9 -------------------------------------------------------------------,JMFF012H01 ...
PATR1 : Integrative Analyses Identify Densely Mapped DERE Regions 方法 : 染色体构象俘获技术 (chromosomeconformation capture , 3C) 双端测序技术 (paired-end sequencing) 末端配对测序 (mate-pair sequencing) 细胞: MCF-7 cells stimulated with E2 for 24 hr
Watch this video to see how to assemble Sanger trace data in SeqMan Pro. After assembly, you can use SeqMan Pros integrated views to see read alignment, assembly coverage, and base quality. You can also edit and annotate the consensus sequence directly in SeqMan Pro.
Download free apps about Biorhythms for Windows: DNA BASER Assembler - affordable sequence assembly, COPD New Patient Evaluation, COPD Follow Up Evaluation, Confidence On-Demand, Clinic H&P Template, Charlie and Arnaud, Asthma Patient Encounter, aOlej Biorhytm, A Day With Charlie, 1st Biorythm
docs] def replace_activities(self): Replace ative flags with Agent states when possible. logger.debug(Running PySB Preassembler replace activities) # TODO: handle activity hierarchies new_stmts = [] def has_agent_activity(stmt): Return True if any agents in the Statement have activity. for agent in stmt.agent_list(): if isinstance(agent, Agent) and agent.activity is not None: return True return False # First collect all explicit active forms self._gather_active_forms() # Iterate over all statements for j, stmt in enumerate(self.statements): logger.debug(%d/%d %s % (j + 1, len(self.statements), stmt)) # If the Statement doesnt have any activities, we can just # keep it and move on if not has_agent_activity(stmt): new_stmts.append(stmt) continue stmt_agents = stmt.agent_list() num_agents = len(stmt_agents) # Make a list with an empty list for each Agent so that later # we can build combinations of Agent forms agent_forms = [[] for a in stmt_agents] for i, agent in ...
GapBlasterは、ゲノムのアセンブリで得られたコンティグを用いて、NNNで繋がったスキャフォールドのクローズを支援するjavaのツール。GUIで動作する。アセンブリで得られたコンティグをblast+/legacy blast/mummerの新井面ツールでスキャホールドにアライメントして、NNNの配列に一致するだろうcontigを絞り込んでいる。論文の表5には、GAGE-Bのデータセットを使って、 Abyss、ABySS2、AllPaths-LG、Bambus2、MSR-CA、SGA、SOAPdenovo、VelvetのNNNが解消された割合がまとめられている。 マニュアル https:/…
COMPASS [for the CDC-6000 series] is the sort of assembler one expects from a corporation whose president codes in octal. -- J.N. Gray. ...
COMPASS [for the CDC-6000 series] is the sort of assembler one expects from a corporation whose president codes in octal. -- J.N. Gray. ...
Пример добавления картинок в ms word. Точно работает с 2007, но по идее должен работать и с остальными постарше. Берёт кучу картинок из каталога с картинками, добавляет в документ и сохраняет в этот же каталог с именем каталога. Lazarus 2.0 + FPC 3.0. ...
The fruit fly Drosophila melanogaster is a principal model organism in metazoan genetics and molecular biology. Here, we describe a BAC-based physical map of chromosomes 2 and 3 constructed as part of the effort to determine the D. melanogaster genome sequence (1). There are five chromosomes (X, 2,3, 4, and Y), and the second and third together account for ∼97 Mb of the ∼120-Mb euchromatic portion of the genome. Several clone-based physical maps have been described previously. Low-resolution yeast artificial chromosome maps of the genome have been produced by polytene chromosome in situ hybridization (2), and cosmid maps of regions of theX chromosome have been made by STS content and fingerprint mapping (3). The most complete previous map is the P1-based map by Kimmerly et al. (4) [also see (5)], constructed by polymerase chain reaction-based STS content mapping and polytene chromosome in situ hybridization. On chromosomes 2 and 3, it comprises 348 sets of contiguously overlapping clones ...
Although second generation sequencing (2GS) technologies allow re-sequencing of previously gold-standard-sequenced genomes, whole genome shotgun sequencing and de novo assembly of large and complex eukaryotic genomes is still difficult. Availability of a genome-wide physical map is therefore still a prerequisite for whole genome sequencing for genomes like barley. To start such an endeavor, large insert genomic libraries, i.e. Bacterial Artificial Chromosome (BAC) libraries, which are unbiased and representing deep haploid genome coverage, need to be ready in place. Result: Five new BAC libraries were constructed for barley (Hordeum vulgare L.) cultivar Morex. These libraries were constructed in different cloning sites (HindIII, EcoRI, MboI and BstXI ) of the respective vectors. In order to enhance unbiased genome representation and to minimize the number of gaps between BAC contigs, which are often due to uneven distribution of restriction sites, a mechanically sheared library was also ...
Until recently, read lengths on the Solexa/Illumina system were too short to reliably assemble transcriptomes without a reference sequence, especially for non-model organisms. However, with read lengths up to 100 nucleotides available in the current version, an assembly without reference genome should be possible. For this study we created an EST data set for the common pond snail Radix balthica by Illumina sequencing of a normalized transcriptome. Performance of three different short read assemblers was compared with respect to: the number of contigs, their length, depth of coverage, their quality in various BLAST searches and the alignment to mitochondrial genes. A single sequencing run of a normalized RNA pool resulted in 16,923,850 paired end reads with median read length of 61 bases. The assemblies generated by VELVET, OASES, and SeqMan NGEN differed in the total number of contigs, contig length, the number and quality of gene hits obtained by BLAST searches against various databases, and contig
Herpesvirus of turkey (HVT) is an alphaherpesvirus that is widely used as a live vaccine against Marek's disease because of its antigenic relationship with Marek's disease virus (MDV). In spite of a similar genome structure, HVT has several unique genes, the functions of which are not completely understood. As a first step in carrying out detailed analysis of the functions of the HVT genes, a full-length infectious bacterial artificial chromosome (BAC) clone of HVT was constructed. DNA from two independent BAC clones, upon transfection into chicken embryo fibroblasts, produced plaques similar to those produced by the wild-type virus. Viruses derived from the BAC clones were stable during in vitro passage, but showed differences in in vitro growth kinetics compared with the wild-type virus. Using a one-step mutagenesis protocol to delete the essential glycoprotein B gene from the HVT genome, followed by construction of the revertant virus, BAC clones of HVT were shown to be amenable to standard
Genome analysis of soybean (Glycine max L.) has been complicated by its paleo-autopolyploid nature and conserved homeologous regions. Landmarks of expressed sequence tags (ESTs) located within a minimum tile path (MTP) of contiguous (contig) bacterial artificial chromosome (BAC) clones or radiation hybrid set can identify stress and defense related gene rich regions in the genome. A physical map of about 2,800 contigs and MTPs of 8,064 BAC clones encompass the soybean genome. That genome is being sequenced by whole genome shotgun methods so that reliable estimates of gene family size and gene locations will provide a useful tool for finishing. The aims here were to develop methods to anchor plant defense- and stress-related gene paralogues on the MTP derived from the soybean physical map, to identify gene rich regions and to correlate those with QTL for disease resistance. The probes included 143 ESTs from a root library selected by subtractive hybridization from a multiply disease resistant soybean
en] The callipyge (CLPG) gene was fine-mapped by linkage analysis to a 4.6-cM chromosome interval on distal ovine OAR18q, flanked by microsatellite markers IDVGA30 and OY3. The OAR18q linkage map and human HSA14q transcript map were aligned by genotyping two bovine-hamster whole-genome radiation hybrid panels with the microsatellite markers, as well as with sequences corresponding to HSA 14q genes. Using Type I loci mapping to the IDVGA30-OY3 interval as anchor points, we have constructed a 1.4-Mb bovine BAC contig containing the IDVGA30-OY3 interval. We demonstrate that the IDVGA30-OY3 interval spans approximately 770 kb and contains at least four genes: YY1, WARS, DLK1, and GTL2 ...
Fingerprint Dive into the research topics of Whole Genome Mate-pair Sequencing of Plasma Cell Neoplasm as a Novel Diagnostic Strategy: A Case of Unrecognized t(2;11) Structural Variation. Together they form a unique fingerprint. ...
A molecular assembler, as defined by K. Eric Drexler, is a proposed device able to guide chemical reactions by positioning reactive molecules with atomic precision. A molecular assembler is a kind of molecular machine. Some biological molecules such as ribosomes fit this definition. This is because they receive instructions from messenger RNA and then assemble specific sequences of amino acids to construct protein molecules. However, the term molecular assembler usually refers to theoretical human-made devices. Beginning in 2007, the British Engineering and Physical Sciences Research Council has funded development of ribosome-like molecular assemblers. Clearly, molecular assemblers are possible in this limited sense. A technology roadmap project, led by the Battelle Memorial Institute and hosted by several U.S. National Laboratories has explored a range of atomically precise fabrication technologies, including both early-generation and longer-term prospects for programmable molecular ...
Once a tiling path has been found, the BACs that form this path are sheared at random into smaller fragments and can be sequenced using the shotgun method on a smaller scale.. Although the full sequences of the BAC contigs is not known, their orientations relative to one another are known. There are several methods for deducing this order and selecting the BACs that make up a tiling path. The general strategy involves identifying the positions of the clones relative to one another and then selecting the least number of clones required to form a contiguous scaffold that covers the entire area of interest. The order of the clones is deduced by determining the way in which they overlap.[15] Overlapping clones can be identified in several ways. A small radioactively or chemically labeled probe containing a sequence-tagged site (STS) can be hybridized onto a microarray upon which the clones are printed.[15] In this way, all the clones that contain a particular sequence in the genome are identified. ...
A hammer bank assembly for use in line printers. The assembly includes an extruded metal rear frame having a uniform thickness and a plurality of machined mounting surfaces which are machined in accurate relationship with respect to one another. A pair of extruded plastic shoes are mounted to the top and bottom of the frame and also include machined surfaces for accurately aligning them with respect to the frame. The shoes include a plurality of mounting slots which are cut by means of a gang cutter. The slots serve to accurately align a plurality of print hammers in the shoes. The hammers are insulated with respect to the frame and the shoes in order to prevent sliding motion and subsequent wearing of the print hammers. Also disclosed are several methods of simplifying the construction procedure of the hammer bank assembly.
Assemble, fit, fasten, and install parts of airplanes, space vehicles, or missiles, such as tails, wings, fuselage, bulkheads, stabilizers, landing gear, rigging and control equipment, or heating and ventilating systems.. Sample of reported job titles: A&P Technician (Airframe and Powerplant Technician), Aircraft Line Assembler, Assembler, Assembly Riveter, Helicopter Technician, Sheet Metal Assembler and Riveter (SMAR), Sheet Metal Mechanic, Structures Mechanic, Structures Technician ...
The molecular marker analysis positioned each deletion breakpoint relative to a defined region on the current MGD/CCR genetic map. This analysis did not identify deletions in addition to the previously characterized 17Pub with breakpoints useful for further refining the ∼0.8-cM functional interval associated with perturbed mesoderm development leading to midgestational lethality of the 1Acrg mutant embryo (Welsh and OBrien 2000). However, a 1.4-Mb BAC contig has been assembled over this critical region and is being used for the identification of candidate genes (Kuriharaet al. 2000). Several of the deletion breakpoints were positioned within the previously characterized functional intervals associated with genes that are essential for newborn survival and normal skeletal and CNS development. In these regions, all of the available D14Mit SSLP markers or STS markers derived from BAC ends were used to construct higher resolution maps (Figures 2 and 3). The ordering of the breakpoints within ...
p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.,/p> ,p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.,/p> ,p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).,/p> ,p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x,sup>64,/sup> + x,sup>4,/sup> + x,sup>3,/sup> + x + 1. The algorithm is described in the ISO 3309 standard. ,/p> ,p class=publication>Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.,br /> ,strong>Cyclic redundancy and other checksums,/strong>,br /> ,a href=http://www.nrbook.com/b/bookcpdf.php>Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993),/a>),/p> Checksum:i ...
Since the initial draft sequence of the human genome was released in 2001, it has become clear that it was not an entirely accurate reconstruction of the genome. Despite significant advances in sequencing and assembly since then, genome sequencing continues to be an inexact process. Genome finishing and validation have remained a largely manual and expensive process, and consequently, many genomes are presented as draft assemblies. Draft assemblies are of unknown quality and potentially contain significant mis-assemblies, such as collapsed repeats, sequence excision, or artificial rearrangements. Too often these assemblies are judged only by contig size, with larger contigs preferred without regard to quality, because it has been difficult to gauge large scale assembly quality. Our new automated software pipeline, amosvalidate, addresses this deficiency and automatically detects mis-assemblies using a battery of known and novel assembly quality metrics. Instead of focusing on a single assembly ...
We offer software for the analysis of DNA data: sequence contig assembly, sequence alignment, molecular fingerprint analysis and phylogetic tree visualisation.
Sequencher - Sequencher works with all automated DNA sequencers and is widely known for its lightning-fast contig assembly, short learning curve, user-friendly editing tools, and superb technical support. First released almost 15 years ago, Sequencher is currently for Mac ::: Download free Software
Sequencher works with all automated DNA sequencers and is widely known for its lightning-fast contig assembly, short learning curve, user-friendly editing
DDBJ released TSA (Transcriptome Shotgun Assembly) data of greater amberjack (Seriola dumerili) which had been submitted by National Research Institute of Aquaculture. The accession numbers are as follows. They are available on getentry or DRASearch. ...
example FT: FT misc_feature 1..53 FT /label=Joiner FT /colour=255 99 71 FT exon 54..22598 FT /label=700917_contig00117 FT /colour=152 251 152 FT misc_feature 22599..22651 FT /label=Joiner FT /colour=255 99 71 FT exon 22652..23638 FT /label=700917_contig00089 FT /colour=152 251 152 FT misc_feature 23639..23691 FT /label=Joiner FT /colour=255 99 71 FT exon 23692..29133 FT /label=RevCompl_700917_contig00127 FT /colour=135 206 250 FT misc_feature 29134..29186 =========== snip ========== ________________________________________ Van: Gowthaman Ramasamy [[email protected]] Verzonden: donderdag 15 december 2011 15:50 Aan: Bossers, Alex; Julian Parkhill; Gowthaman Ramasamy CC: [email protected] Onderwerp: Re: [Artemis-users] Customizing crunch file in ACT... Thats a wonderful idea. In fact I already load the contigs FT track (from Abacass). But, it never occurred to me that we can modify it to load linker information as well. After Alexs email, I am started to ...
I have a RNA-Seq data in which I have to construct the KEGG Pathway for DGE between two samples. I also have nucleotide sequences (contigs) in the fasta format (.fa) file. Kindly tell me how to assign the KO IDs to these nucleotide sequences. Also help me in construction of pathways either using KEGG, Cytoscape or any other pathway network builder software/server. . ...
Larger insertions and deletions are found by looking at variation in mate pair distances in the 2x50 mate pair libraries. These data are included in separate files for each of three coverage values: 2.2x, 4.0x, 5.6x, and 8.4 ...
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Finally, the assembly itself is done using programs such as ABySS or Spades or SOAPdenovo2, which produce contig files and scaffold files. For each assembly, quast produces an reports with extensive statistics that can guide the choice of which assembly is best, or which assemblies should be repeated with different a parameters for improvement ...
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If you would like to experiment further, you can download the fly genome contigs and psl alignment file. After downloading the example data, you install PEP_scaffolder program into the example diretory and type sh PEP_scaffolder/PEP_scaffolder.sh -d PEP_scaffolder/ -i fly.psl -j fly_contig.fasta . A file named PEP_scaffolder.fasta is the scaffolding result. If you have any trouble using PEP_scaffolder, then please first follow the steps in our Documentation before contacting us.. ...
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Nasal Cavity Sections (/Rhythmyx/assembler/render?sys_contentid=34273&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid= sys_dependentvariantid=639 sys_dependentid=34273 inlinetype=rxhyperlink rxinlineslot=103 sys_dependentid=34273 sys_siteid= sys_folderid=), Infusion (/Rhythmyx/assembler/render?sys_contentid=34273&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid= sys_dependentvariantid=639 sys_dependentid=34273 inlinetype=rxhyperlink rxinlineslot=103 sys_dependentid=34273 sys_siteid= sys_folderid=) ...
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Read a single 8-bit I/O port. This function is provided as an inline assembler macro, and will be optimized down to a single opcode when you optimize your program. ...
Carlos Filipe Pereira, Chang, B., Gomes, A., Bernitz, J. M., Papatsenko, D., Niu, X., Swiers, G., Azzoni, E., de Bruijn, M. F. T. R., Schaniel, C., Lemischka, I. R. & Moore, K. A., 2016 mar 7, I : Developmental Cell. 36, 5, s. 525-539 15 s.. Forskningsoutput: Tidskriftsbidrag › Artikel i vetenskaplig tidskrift ...
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1995). "A YAC contig map of the human genome". Nature. 377 (6547 Suppl): 175-297. doi:10.1038/377175a0 (inactive 2021-01-18). ... "A YAC contig map of the human genome. Nature 1995 Sep; 377(6547 Suppl):175-297. Cited 410 times according to Google Scholar ... He contributed to the first physical map of the Human Genome at Genethon and at Genset Corporation as a member of Daniel Cohen ... Mapping the whole human genome by fingerprinting yeast artificial chromosomes. Cell. 1992 Sep 18;70(6):1059-68. Cited 229 times ...
... the physical maps were constructed. The physical maps were integrated together with genetic maps to identify contig positions ... The small pieces are then assembled into contigs by overlapping them. Next, using the map from the first step the contigs are ... The assembly was then polished with the help of Illumina paired-end reads by mapping them to the contigs using BWA-MEM. By ... For Oryza Sativa a total of 3,401 mapped clones in a minimum tiling path were selected from the physical map and assembled. One ...
This process produces a contig map of the locus and is known as chromosome walking. With the completion of genome sequencing ... The screen is carried out by mapping mutants of a biological process until no new genes/gene mutations can be found. Christiane ... SNPs are the preferred traits for mapping since they are very frequent, on the order of one difference per 1000 base pairs, ... Depending on the size of the mapping population, the mutant allele can be narrowed down to a small region (. ...
2002). "Genomic organisation of the approximately 1.5 Mb Smith-Magenis syndrome critical interval: transcription map, genomic ... contig, and candidate gene analysis". Eur. J. Hum. Genet. 9 (12): 892-902. doi:10.1038/sj.ejhg.5200734. PMID 11840190. ...
"Anchoring 9,371 maize expressed sequence tagged unigenes to the bacterial artificial chromosome contig map by two-dimensional ... 1997 ). Mapping probes: SSR p-umc1022 (Sharopova et al. 2002 ); Overgo (physical map probe) PCO06449 (Gardiner et al. 2004 ). ... 2011 ). Genetic mapping using recombinant inbred lines derived from maize inbred lines B73 and Mo17 showed that a 3.9 kb cis- ... "Development and mapping of SSR markers for maize". Plant Molecular Biology. 48 (5-6): 463-81. doi:10.1023/a:1014868625533. PMID ...
Stage 4: contig construction. SPAdes outputs contigs and allows to map reads back to their positions in the assembly graph ... SOAPdenovo Largest contig: IDBA-UD > SPAdes > > EULER-SR > Velvet= E+V-SC > Velvet-SC > SOAPdenovo Mapped genome (%): SPAdes > ... If P is a non-branching path (h-path), then SPAdes maps every edge in P to an edge projection in Q and removes P from the graph ... dipSPAdes constructs longer contigs by taking advantage of divergence between haplomes in repetitive genome regions. Afterwards ...
"Construction of a 750-kb bacterial clone contig and restriction map in the region of human chromosome 21 containing the ... BACs can also be utilized to detect genes or large sequences of interest and then used to map them onto the human chromosome ...
... a 1.1-Mb BAC contig, a partial transcript map and 15 new repeat polymorphisms in a tumour-suppressor region". European Journal ... Baysal BE, Willett-Brozick JE, Taschner PE, Dauwerse JG, Devilee P, Devlin B (Feb 2001). "A high-resolution integrated map ...
Applications of PQ trees include creating a contig map from DNA fragments[citation needed], testing a matrix for the ...
... chromosome chromosomal translocation cloning congenital disorder contig craniosynostosis cystic fibrosis cytogenetic map ... gene library gene mapping gene pool gene therapy gene transfer genetic code ATGC genetic counseling genetic linkage genetic map ... karyotype knockout leukemia List of human genetic disorders locus LOD score lymphocyte malformation Gene mapping marker ... sequence nucleus oligo oncogene oncovirus p53 Particulate inheritance theory patent pedigree peptide phenotype physical map ...
... maps reads to a reference genome or performs de novo assembly of the reads into transcript contigs and supercontigs The first ... sequences are mapped against 16S rRNA Greengenes v13.5 database using SOAP2, while for functional analysis sequences are mapped ... Metatranscriptomic reads are mapped against databases using alignment tools, such as Bowtie2, BWA, and BLAST. Then, the results ... Remaining reads are then mapped on NCBI databases by using BLAST and MegaBLAST tools and classified by their bitscore. Higher ...
Consensus sequence Conservative change Conserved sequence Constant region Constitutive gene Contig Contig map Contig maps ... Lysogen Lysogenic Lysogenic bacterium Macromolecule Macrorestriction map Malformation Manx Mapping Mapping function Mapping ... Deletion Deletion chromosome Deletion map Deletion mapping Deme (Biology) Dementia Denaturation Denaturation map Denominator ... Gene expression Gene family Gene flow Gene frequency Gene fusion Gene interaction Gene library Gene locus Gene map Gene mapping ...
Contigs therefore provide the framework for hierarchical sequencing. The assembly of a contig map involves several steps. First ... and a scaffold-consisting of contigs and gaps-that covers the map region is often the first result. The gaps between contigs ... Contig can also refer to the overlapping clones that form a physical map of a chromosome when the top-down or hierarchical ... If gaps between contigs remain after STS landmark mapping and restriction fingerprinting have been performed, the sequencing of ...
It uses the existing cloned fragments in genomic libraries to form contigs. Through cloning the partially digested fragments ... Genetic mapping, another approach of gene mapping, can provide markers needed for the physical mapping. However, as the former ... which is to be classified to low-resolution mapping rather than a high-resolution mapping. Restriction mapping is a top-down ... High-resolution physical mapping could resolve hundreds of kilobases to a single nucleotide of DNA. A major technique to map ...
These profiles can be compared to results of an actual denaturation experiment to map the contigs. To this end, more recently ... Denaturation Mapping is a form of optical mapping, first described in 1966. It is used to characterize DNA molecules without ... 1966)."A denaturation map of the lamda phage DNA molecule determined by electron microscopy". Journal of Molecular Biology 18: ... It was not uncommon to ribosomal DNA and compare the resulting maps of related organisms not unlike 16s rRNA identification ...
By this approach, physical map contigs can be "anchored" onto a genetic map. The clones used in the physical map contigs can ... There are two distinctive types of "Maps" used in the field of genome mapping: genetic maps and physical maps. While both maps ... The two factors are interlinked, as a larger mapping population could increase the "resolution" of the map and prevent the map ... This type of mapping is more accurate than genetic maps. In the early 1950s the prevailing view was that the genes in a ...
... with physical maps such as optical or synteny maps. Some software, like ABySS and SOAPdenovo, contain gap filling algorithms ... The next step is to then bridge the gaps between these contigs to create a scaffold. This can be done using either optical ... Optical mapping is the process of immobilizing the DNA on a slide and digesting it with restriction enzymes. The fragment ends ... They were able to greatly increase N50 contig length and decrease gap length, and even to close one microbial genome with this ...
"Efficient construction of a physical map by fiber-FISH of the CLN5 region: refined assignment and long-range contig covering ... 2007). "Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3 (1): 89. doi: ...
To serve as scaffolds for assembly, assembled sequence contigs can be scanned for restriction sites in silico using known ... high-resolution restriction maps from single, stained molecules of DNA, called "optical maps". By mapping the location of ... Individual optical maps are combined to produce a consensus, genomic optical map. DNA molecules were fixed on molten agarose ... Initially, the optical mapping system has been used to construct whole-genome restriction maps of bacteria, parasites, and ...
... and integration of genetic and physical maps). Along his career, Korol has developed methods and tools for genetic mapping of ... contig assembly algorithms for BAC libraries based on fingerprinting or DNA-DNA hybridization data, ... Another complementary problem to reconstructing genetic maps is ensemble a consensus map from data produced by different labs, ... Currently Korol's group is responsible for developing new methodology for physical genome mapping in complex cereal genomes in ...
For a bacterium containing a single chromosome, a genome project will aim to map the sequence of that chromosome. For the human ... The resulting (draft) genome sequence is produced by combining the information sequenced contigs and then employing linking ... Scaffolds are positioned along the physical map of the chromosomes creating a "golden path". Originally, most large-scale DNA ... Historically, when sequencing eukaryotic genomes (such as the worm Caenorhabditis elegans) it was common to first map the ...
To solve this issue, a new technique was developed to allow for facilitation of mapping of pericentromeric regions. They key ... it becomes increasingly difficult to disassemble sequence contigs using whole genome shotgun approaches. ... Nowadays, these duplications prefer to map to the pericentromeric regions in the modern human and chimpanzee. There has been a ... Scientist have attempted to map the location of these segmental duplications, but they run into issues of accurate sequencing ...
Metrics to assess the quality of a de novo assembly include median contig length, number of contigs and N50. Genome guided: ... In each case multiple stages of the embryo were studied, allowing the entire process of development to be mapped on a cell-by- ... Expression is quantified by counting the number of reads that mapped to each locus in the transcriptome assembly step. ... Expression can be quantified for exons or genes using contigs or reference transcript annotations. These observed RNA-Seq read ...
... assemble into contigs Bioinformatics Cloning vector Computational biology Expression vector List of open source bioinformatics ... software Restriction map Vector (molecular biology) Vector DNA http://www.basic.northwestern.edu/VectorNTI/Documentation/ ...
By this approach, physical map contigs can be "anchored" onto a genetic map. The clones used in the physical map contigs can ... There are two distinctive types of "Maps" used in the field of genome mapping: genetic maps and physical maps. While both maps ... The two factors are interlinked, as a larger mapping population could increase the "resolution" of the map and prevent the map ... Gene mapping[edit]. Researchers begin a genetic map by collecting samples of blood or tissue from family members that carry a ...
Mapping of an ensemble of sequences on a reference sequence between a reference sequence and contigs, between two sequences or ... This covers sequence assembly, mapping, annotation transfer and identification of protein domains, comparative genomics, ... genomic maps according to their expression values and highlight the corresponding reactions in interactive metabolic KEGG maps ... Fisher test Collect and visualize all functional data in exportable tables and maps Genostar's MicroB database is constructed ...
... construction of an integrated YAC/PAC contig and a partial transcriptional map in the region of chromosome 2q13". Genomics. 41 ... 2002). "A sequence-based map of the nine genes of the human interleukin-1 cluster". Genomics. 79 (5): 718-25. doi:10.1006/geno. ... Nicklin MJ, Weith A, Duff GW (1994). "A physical map of the region encompassing the human interleukin-1 alpha, interleukin-1 ...
... physical chromosome mapping MeSH E05.393.183.620.160 - contig mapping MeSH E05.393.183.620.405 - radiation hybrid mapping MeSH ... epitope mapping MeSH E05.601.690.650 - two-hybrid system techniques MeSH E05.624.850.830 - subrenal capsule assay MeSH E05.680. ... peptide mapping MeSH E05.393.760.705.685.690 - protein footprinting MeSH E05.393.760.710 - sequence analysis, rna MeSH E05.472. ... nucleotide mapping MeSH E05.196.181.400.454.655.100 - blotting, northern MeSH E05.196.181.400.454.655.150 - blotting, southern ...
"A YAC contig and an EST map in the pericentromeric region of chromosome 13 surrounding the loci for neurosensory nonsyndromic ... "A radiation hybrid map of 48 loci including the clouston hidrotic ectodermal dysplasia locus in the pericentromeric region of ... "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. doi:10.1038/ ...
Explicit read mapping and de novo assembly are typically slow. Reordering-based FASTQ compressors first cluster reads that ... substrings and then independently compress reads in each cluster after reordering them or assembling them into longer contigs, ... A quality value Q is an integer mapping of p (i.e., the probability that the corresponding base call is incorrect). Two ... earlier used a different mapping, encoding the odds p/(1-p) instead of the probability p: Q solexa-prior to v.1.3 = − 10 log 10 ...
A high resolution map can be created by sequencing both ends of inserts from several clones in a genomic library. This map ... Any new overlapping clones can then be sequenced forming a contig. This technique, called chromosome walking, can be exploited ... One major use of genomic libraries is hierarchichal shotgun sequencing, which is also called top-down, map-based or clone-by- ...
Overlapping reads form contigs; contigs and gaps of known length form scaffolds. ... McElheny V (2010). Drawing the map of life : inside the Human Genome Project. New York NY: Basic Books. ISBN 978-0-465-04333-0. ... Paired end reads of next generation sequencing data mapped to a reference genome. ... genome mapping, data storage, and bioinformatic analysis most widely used in the following quarter-century of research.[19][20] ...
... construction of an integrated YAC/PAC contig and a partial transcriptional map in the region of chromosome 2q13". Genomics. 41 ... 2002). "A sequence-based map of the nine genes of the human interleukin-1 cluster". Genomics. 79 (5): 718-25. doi:10.1006/geno. ... Nicklin MJ, Weith A, Duff GW (1994). "A physical map of the region encompassing the human interleukin-1 alpha, interleukin-1 ...
... or by using direct repeat sequences in partially assembled CRISPR arrays from contigs (overlapping DNA segments that together ... "High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates". PLoS ...
Contigs can be linked together into scaffolds by following connections between mate pairs. The distance between contigs can be ... a b c Dear, P. H. Genome Mapping. Encyclopedia of Life Sciences, 2005. doi:10.1038/npg.els.0005353. ... a low-resolution physical map of the genome is made prior to actual sequencing. From this map, a minimal number of fragments ... Depending on the size of the gap between contigs, different techniques can be used to find the sequence in the gaps. If the gap ...
"Sequence Alignment/Map Format Specification" (PDF).. *^ Brudno M; Malde S; Poliakov A; Do CB; Couronne O; Dubchak I; Batzoglou ... where sequences are aligned to find overlap so that contigs (long stretches of sequence) can be formed.[35] Another use is SNP ... "Mapping the protein universe". Science. 273 (5275): 595-603. Bibcode:1996Sci...273..595H. doi:10.1126/science.273.5275.595 ...
Features include chromatogram editing, end clipping, and vector trimming, sequence assembly and contig editing, aligning cDNA ... "Equine Multiple Congenital Ocular Anomalies maps to a 4.9 megabase interval on horse chromosome 6". BMC Genet. 9: 88. doi: ... against genomic templates, sequence alignment and editing, alignment of contigs to each other with ClustalW, MUSCLE, or built- ...
Mapping color-space reads to a color-space reference can properly utilize the two-base encoding rules where only adjacent color ... Quality filtering of the reads can deliver higher raw accuracy reads which when aligned to form color contigs can deliver ... Patent: Reagents,Methods and Libraries for Bead-Based Sequencing Article: A high-resolution, nucleosome position map of C. ...
There was uniform mapping of reads to genome; at least one read mapped to >88% of the genome. The relatively long reads allowed ... Longer patterns of methylation are often lost because smaller contigs still need to be assembled. Transcriptomics is the study ...
... which ultimately helps resolve the placement of contigs. Contigs present in the same chromosome will exhibit the same ... and other large chromosomal abnormalities are likely to share this mapping resolution (if breakpoint fine-mapping is performed ... Misoriented contigs are present where strand inheritance changes from one homozygous state to the other (ex. WW to CC, or CC to ... Scaffolds, successive contigs intersected by a gap, can be localized in the same manner. The same principle of using strand ...
Sequence Alignment/Map(SAM) (.sam), binary version of SAM (.bam), ACE (.ace), FASTQ (.fastq) Phylogenetic trees: Newick (.nwk ... and edit phylogenetic trees Combine various algorithms into custom workflows with UGENE Workflow Designer Contigs assembly with ... results in a nucleic acid sequence with UGENE Query Designer PCR in silico for primer designing and mapping Spade de novo ... for PCR primer design Plasmid construction and annotation Cloning in silico by designing of cloning vectors Genome mapping of ...
... editing and annotating Contig assembly and chromatogram editing including comparison to a reference sequence to identify ... for viewing restriction cut sites in tables and on linear and circular maps. A Subcloning tool for the assembly of constructs ...
MyDefrag CLI -- Can execute script via CLI but displays disk map. MyDefrag Scripts -- Runs exclusively via scripts. Included ... Russinovich, Mark (July 4, 2016). "Contig v1.8". Windows Sysinternals. Microsoft. Retrieved June 9, 2011. CS1 maint: ...
... they were able to generate 6.58 million contigs greater than 500 bp for a total contig length of 10.3 Gb and a N50 length of ... "Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps". G3. 4 (7): 1339-46. doi:10.1534 ... Misassemblies can also involve the combination of sequences from more than one species into chimeric contigs. There are several ... Metagenomic analysis pipelines use two approaches in the annotation of coding regions in the assembled contigs. The first ...
"SNP linked to Gene (geneID:84865) Via Contig Annotation". www.ncbi.nlm.nih.gov. Retrieved 2016-05-01. "RBPDB: The database of ... "Microarray Data :: Allen Brain Atlas: Human Brain". human.brain-map.org. Retrieved 2016-05-01. "EST Profile - Hs.430199". www. ...
The map of a particular pathway and a comparison between two kinds of microbes can be shown in the pathway browser. The enzyme ... having a unique label per contig, (3) preferably gene predictions should be present (in this case, accepted formats include ... The Pathway Browser lets users to navigate the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway maps displaying predicted ... Bates, J. T.; Chivian, D.; Arkin, A. P. (2011). "GLAMM: Genome-Linked Application for Metabolic Maps". Nucleic Acids Research. ...
... genome.cshlp.org/content/18/11/1851 Mapping short DNA sequencing reads and calling variants using mapping quality scores. ... technology these reads are short compared to the length of a genome therefore the reads must be assembled into longer contigs. ... GS Reference Mapper maps short reads to a reference genome, generating a consensus sequence. The software is able to generate ... It uses the MaxMapper algorithm to map the colour space reads. Beckman Coulter (now Danaher) has previously manufactured chain ...
PMID 22068540.CS1 maint: uses authors parameter (link) "DIMACS Workshop on Combinatorial Methods for DNA Mapping and Sequencing ... Huang, Xiaoqiu (1992-09-01). "A contig assembly program based on sensitive detection of fragment overlaps". Genomics. 14 (1): ... assembly of overlapping reads into larger contigs, and 4) repeat. These algorithms typically do not work well for larger read ...
Firstly, contigs were generated de novo, secondly, the contigs were ordered and concatenated into supercontigs, and, thirdly, ... These reads were then mapped to the long reads using BLASR. The results from the ABySS assembly were used to create the ... The initial de novo assembly of contigs was achieved in parallel using Velvet, which assembles contigs by manipulating De ... which only uses long contigs with the edges of the graph representing the putative genomic connection between the contigs. The ...
Projector: automatic contig mapping for gap closure purposes Projector 2: contig mapping for efficient gap-closure of ... contig mapping can also refer to... contig mapping ... contig mapping. in Oxford Dictionary of Biochemistry and ... A technique used in projects such as the Human Genome Project to enable the physical map of (part of) a chromosome to be ... The method relies on the use of overlapping clones, referred to as contigs. ...
... electronic physical map anchoring tool) that combines BAC contig information generated by FingerPrinted Contig with results of ... Results show that a one dimensional pool screening can be sufficient to anchor a BAC contig while reducing the number of PCR by ... Elephant was evaluated during the construction of a physical map of chromosome 3B of hexaploid wheat. ... Anchored physical maps represent essential frameworks for map-based cloning, comparative genomics studies, and genome ...
Long-range mapping and construction of a YAC contig within the cat eye syndrome critical region ... Physical mapping between the S and HLA-E genes in the human MHC class I region: Construction of a BAC, PAC, and cosmid contig. ... Genetic mapping of the branchio-oto-renal syndrome and construction of YAC contig spanning the BOR region on chromosome 8q. ... Construction of a YAC contig and STS map spanning at least 10 cM in 1q41, the critical region of Usher II gene. American ...
Retrieved from "http://www.webref.org/wiki/index.php?title=Contiguous_(contig)_map" ... View source for Contiguous (contig) map. From WebRef.org. ← Contiguous (contig) map ...
Using Type I loci mapping to the IDVGA30-OY3 interval as anchor points, we have constructed a 1.4-Mb bovine BAC contig ... Reference : Fine-mapping and construction of a bovine contig spanning the ovine callipyge locus.. ... Fine-mapping and construction of a bovine contig spanning the ovine callipyge locus. ... The OAR18q linkage map and human HSA14q transcript map were aligned by genotyping two bovine-hamster whole-genome radiation ...
"Mapping of the mouse hyh gene to a YAC/BAC contig on proximal Chromosome 7, Mammalian Genome" on DeepDyve, the largest online ... Mapping of the mouse hyh gene to a YAC/BAC contig on proximal Chromosome 7. Mapping of the mouse hyh gene to a YAC/BAC contig ... Mapping of the mouse hyh gene to a YAC/BAC contig on proximal Chromosome 7. Chae, Teresa H.; Allen, Kristina M.; Davisson, ... map. Our physical map and transcript map may be useful for positional cloning of genes in this unusually gene-rich region of ...
Find out information about Contig map. A region of chromosome defined by its hybridization to one or more cloned ... Contig map , Article about Contig map by The Free Dictionary https://encyclopedia2.thefreedictionary.com/Contig+map ... contig. (redirected from Contig map). Also found in: Medical. contig. [kən′tig] (genetics) A region of chromosome defined by ... The matching results can be displayed in matrix or table form, as well as in dendrograms and contig maps.. Bio Image announces ...
Bowtie2 mapping of (several, long) contigs in fasta to a reference sequence - contig sequences only mapped as 60 bp Ive got ... Map de individual contigs to the reference using BLAT or BLAST or similar. Just layout the contigs in order and use these as ... so we have contigs built de novo or contigs built according to a close reference. I would like to work with the de novo contigs ... It is for option 1. The mapping of contigs to a reference using BLAT (BLAT/BLAST section). From BLAT generate the syntenylist ( ...
Interpret coverage from mapping back de-novo assembly Dear all, I have assembly my reads with MEGAHIT to get final contigs. ... Mapping using assembled contigs Hi there, I have just downloaded some genome assemblies from NCBI that are assembled at the ... Why map reads back to assembly? Hi! I wanted to know why (and if) is useful to map the reads back to the assembled sequence. ... denovo assembly and mapping Does anyone know why when doing a de novo assembly of a bacterial isolate and then mapping back t ...
Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome ( ... Anchoring physical map with genetic maps. In order to anchor the contig map with the genetic map, a total of 337 polymorphic ... contig map with the other available genetic maps of chickpea for locating all mapped genes and QTLs to physical map contigs. ... Anchoring of physical map with genetic maps. For anchoring the physical map with the genetic map, a set of 337 BAC clones ...
CMAP: Contig mapping and analysis package, a relational database for chromosome reconstruction // Cabios.-1992.-v.8.-N 5.-P. ... CMAP: Contig mapping and analysis package, a relational database for chromosome reconstruction // Cabios.-1992.-v.8.-N 5.-P. ...
Mapping of unplaced contigs of the mouse genome. The current mouse reference genome assembly (mm10/GRCm38.p5) consists of 22 ... Mapping of unplaced sequences in the CC. (A) QTL scan demonstrating successful localization of GL456378, a contig not localized ... An example of its value is the mapping of unplaced contigs, which improves the accuracy of the mouse reference genome. ... Mapping resolution of the unplaced contigs is relatively high, given the small size of the CC sequenced population (median ...
If a read can map to an alternate contig, then it is mapped to the alternate contig as a primary alignment. For those reads ... How to) Map and clean up short read sequence data efficiently * (How to) Map reads to a reference with alternate contigs like ... In addition to mapped alternate contig records, the ALT index also contains decoy contig records as unmapped SAM records. This ... BWA takes the reads that it cannot map to the primary assembly and attempts to map them to the alternate contigs. ...
Contigs therefore provide the framework for hierarchical sequencing. The assembly of a contig map involves several steps. First ... and a scaffold-consisting of contigs and gaps-that covers the map region is often the first result. The gaps between contigs ... Contig can also refer to the overlapping clones that form a physical map of a chromosome when the top-down or hierarchical ... If gaps between contigs remain after STS landmark mapping and restriction fingerprinting have been performed, the sequencing of ...
1995). "A YAC contig map of the human genome". Nature. 377 (6547 Suppl): 175-297. doi:10.1038/377175a0 (inactive 2021-01-18). ... "A YAC contig map of the human genome. Nature 1995 Sep; 377(6547 Suppl):175-297. Cited 410 times according to Google Scholar ... He contributed to the first physical map of the Human Genome at Genethon and at Genset Corporation as a member of Daniel Cohen ... Mapping the whole human genome by fingerprinting yeast artificial chromosomes. Cell. 1992 Sep 18;70(6):1059-68. Cited 229 times ...
... to close the gaps between contigs with other contig sequences after scaffolding contigs using an optical map. The results, ... to close the gaps between contigs with other contig sequences after scaffolding contigs using an optical map. The results, ... to close the gaps between contigs with other contig sequences after scaffolding contigs using an optical map. The results, ... to close the gaps between contigs with other contig sequences after scaffolding contigs using an optical map. The results, ...
Contig Mapping * Denmark * Feces / microbiology * Gastrointestinal Tract / microbiology* * Genes, Bacterial / genetics * Genes ...
Contig Mapping * Cyclotides / biosynthesis* * Expressed Sequence Tags* * Flow Cytometry * Gene Expression Profiling ... High-quality ESTs were identified, 1,117 in total, from leaf cDNAs and assembled into 502 contigs, comprising 202 consensus ...
High resolution physical mapping of a 6.7 Mb YAC contig spanning a region critical for the monosomy 21 phenotype in 21q21.3- ... Genomics: international journal of gene mapping and nucleotide sequencing. - San Diego, Calif. ...
A high-density STS map based on a single contig of YAC and P1 clones in the chromosome 8p12-p21 region. Genomics. 1997 Apr 1;41 ... A high-density STS map based on a single contig of YAC and P1 clones in the chromosome 8p12-p21 region. In: Genomics. 1997 ; ... Fingerprint Dive into the research topics of A high-density STS map based on a single contig of YAC and P1 clones in the ... A high-density STS map based on a single contig of YAC and P1 clones in the chromosome 8p12-p21 region. / Mitsuda, Noriaki; ...
In this study we demonstrate their utility for locating fingerprint contigs (FPCs) to the genetic map. To derive SNP and InDel ... In this study we demonstrate their utility for locating fingerprint contigs (FPCs) to the genetic map. To derive SNP and InDel ... In this study we demonstrate their utility for locating fingerprint contigs (FPCs) to the genetic map. To derive SNP and InDel ... In this study we demonstrate their utility for locating fingerprint contigs (FPCs) to the genetic map. To derive SNP and InDel ...
Chromosome 7 contig map: The contig map of chromosome 7 was built in five steps: *. At the beginning of this work 28 DNA ... Generation of the contig map: The contig map was generated by radioactive labeling of one of the probes described above ... Spacing of markers on the contig map: The contig map cannot give a reliable estimate of the distance between the markers on the ... Random breakage mapping: The contig map gives the order of markers, but it does not give physical distances, except as an ...
BAC contig map of a region containing a cluster of apyrase genes. The map indicates the location of the Mtapy1, Mtapy3, and ... The map locations of the other two apyrase-associated contigs in soybean were not determined. It is significant that the ... Placing BAC Contigs onto the Soybean Genetic Map. GS50 and GS52 hybridizations potentially revealed more than one location in ... Genetic Mapping of Apyrases. To determine the genetic map position of the apyrase cluster (Mtapy1, Mtapy3, and Mtapy4) and of ...
454 contigs not mapping to a genomic sequence; B) genomic contigs not mapping to a 454 contig; C and J) 454 contigs with an ... A descriptive analysis of planarian splice sites was conducted on those Smed454 contigs that mapped univocally to the current ... HSPs on 454 contigs supporting a pair of genomic contigs, which could then be merged into a larger genomic scaffold. All ... Analysis of intronic features and splice sites on a set of 90e contigs. A) Distribution of the number of putative introns per ...
Contig gap closure is performed by walking experiments using STSs developed from the end sequences of the clone inserts. © 1997 ... The strategy we are following involves establishing a high density framework map of the order of 15 markers per Megabase using ... which are assembled into sequence-ready contigs by restriction enzyme fingerprinting and sequence tagged site (STS) content ... radiation hybrid (RH) mapping. The markers are then used to identify large-insert genomic bacterial clones covering the ...
A random cosmid contig approach to gene-mapping [Abstract]. Cytogenetics and Cell Genetics 46(1-4), pp. 581. (10.1159/000316989 ... A random cosmid contig approach to gene-mapping [Abstract]. Cytogenetics and Cell Genetics 46(1-4), pp. 581. (10.1159/000316989 ... A random cosmid contig approach to gene-mapping. Cytogenetics and Cell Genetics 46(1), pp. 581-581. ... A random cosmid contig approach to gene-mapping. Cytogenetics and Cell Genetics 46(1), pp. 581-581. ...
van Hijum, S. A. F. T., Zomer, A. L., Kuipers, O. P., & Kok, J. (2005). Projector 2: contig mapping for efficient gap-closure ... van Hijum, S. A. F. T., Zomer, A. L., Kuipers, O. P., & Kok, J. (2003). Projector: automatic contig mapping for gap closure ...
Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid ... genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of ... 512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of ... and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We ...
... mapping of genomic 454 reads along the contig; C) mapping of trascriptomic Illumina reads along the contig and the coverage ... Genomic contigs resulting from de-novo assembling of all 454 genomic reads (fasta format). ... Contig number and ID; primer pairs, amplicon length, description and related fasta sequences. ... Gene structure of contig 2509 (GADD45). A) gene, mRNA and CSD annotation; B) ...
Efficient Indexed Alignment of Contigs to Optical Maps. Muggli, Martin D. (et al.) ...
  • A technique used in projects such as the Human Genome Project to enable the physical map of (part of) a chromosome to be determined. (oup.com)
  • We have also used 15 loci to construct a yeast artificial chromosome contig, which encompasses about half of the region critical to the production of the CES phenotype (centromere to D22S57). (eurekamag.com)
  • en] The callipyge (CLPG) gene was fine-mapped by linkage analysis to a 4.6-cM chromosome interval on distal ovine OAR18q, flanked by microsatellite markers IDVGA30 and OY3. (ac.be)
  • A contig of yeast artificial chromosome (YAC) clones and bacterial artificial chromosome (BAC) clones spanning this entire region has been developed, and a number of potential candidate genes for hyh within this interval have been identified. (deepdyve.com)
  • From BLAT generate the syntenylist (baiscally the orientation layout of contigs) which you can use subsequently to Join (you find it in the Artemis/MUMmer section) in an artificial chromosome using spacers and/or linker providing an EMBL layout file as well for inspecting in for instance ACT or Artemis of Sanger. (biostars.org)
  • Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). (springer.com)
  • Contig can also refer to the overlapping clones that form a physical map of a chromosome when the top-down or hierarchical sequencing strategy is used. (wikipedia.org)
  • the minimum number of clones that form a contig that covers the entire chromosome comprise the tiling path that is used for sequencing. (wikipedia.org)
  • Since these clones should cover the entire genome/chromosome, it is theoretically possible to assemble a contig of BACs that covers the entire chromosome. (wikipedia.org)
  • CMAP: Contig mapping and analysis package, a relational database for chromosome reconstruction // Cabios. (ac.ru)
  • Specifically, the tutorial uses BWA-MEM to index and map simulated reads for three samples to a mini-reference composed of a GRCh38 chromosome and alternate contig ( sections 1-3 ). (broadinstitute.org)
  • We have constructed a yeast artificial chromosome (YAC) and P1 contig in the 8p12-p21 region. (elsevier.com)
  • The amplification primers for all mapped InDel and SNP loci, the diversity information for SNPs and InDels, and the corresponding overgoes to anchor bacterial artificial chromosome (BAC) contigs are provided as genetic resources. (elsevier.com)
  • As part of the ongoing Candida albicans Genome Project, we have constructed a complete sequence-tagged site contig map of chromosome 7 , using a library of 3840 clones made in fosmids to promote the stability of repeated DNA. (genetics.org)
  • In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC) library for the nurse shark, Ginglymostoma cirratum. (nih.gov)
  • Diversity maps," which depict the levels and patterns of variation in different gene pools, shed light on relationships of allelic diversity with chromosome organization, and suggest possible locations of genomic regions that are under selection due to major gene effects (some of which may be revealed by quantitative trait locus mapping). (plantphysiol.org)
  • We seek to provide a detailed picture of the structure, function, and evolution of the genome of sorghum and its relatives, together with molecular tools such as locus-specific sequence-tagged site DNA markers and bacterial artificial chromosome contigs that will have enduring value for many aspects of genome analysis. (plantphysiol.org)
  • Comparisons of the physical map with consensus genetic linkage map revealed that ≈20% of chromosome 5B recombination occurs in this region. (pnas.org)
  • Using a set of interspecific SNPs, 11 randomly selected and 77 SNPs that are putatively associated with the homeologous chromosome pair 12 and 26, we mapped 77 SNPs into two linkage groups representing these chromosomes, spanning a total of 236.2 cM in an interspecific F2 population ( G. barbadense 3-79 × G. hirsutum TM-1). (g3journal.org)
  • A primary goal of the Human Genome Project is to make a series of descriptive diagrams maps of each human chromosome at increasingly finer resolutions. (lsu.edu)
  • A genome map describes the order of genes or other markers and the spacing between them on each chromosome. (lsu.edu)
  • A genetic linkage map shows the relative locations of specific DNA markers along the chromosome. (lsu.edu)
  • This was the first successful gene mapping work and provides important evidence for the Boveri-Sutton chromosome theory of inheritance . (wikipedia.org)
  • The map shows the relative positions of allelic characteristics on the second Drosophila chromosome. (wikipedia.org)
  • While the physical map could be a more "accurate" representation of the genome, genetic maps often offer insights into the nature of different regions of the chromosome, e.g. the genetic distance to physical distance ratio varies greatly at different genomic regions which reflects different recombination rates, and such rate is often indicative of euchromatic (usually gene-rich) vs heterochromatic (usually gene poor) regions of the genome. (wikipedia.org)
  • Chromosome mapping is the assignment of genes to specific locations on a chromosome. (encyclopedia.com)
  • A detailed chromosome map also provides methods to study how genes are segregated and how genetic heterogeneity (variation between a particular gene maternally inherited and the same gene with a slightly different sequence that is paternally inherited) can help identify disease genes. (encyclopedia.com)
  • This method allows scientists to identify which chromosome contains the gene, and represents one of the first mapping methods used by scientists. (encyclopedia.com)
  • This later became known as the Law of Independent Assortment, a concept that enhanced chromosome mapping techniques. (encyclopedia.com)
  • A physical map orders genes or markers along the DNA strand of a chromosome. (encyclopedia.com)
  • Construction of a rabbit bacterial artificial chromosome (BAC) library: application to the mapping of the major histocompatibility complex to position 12q1.1. (ebscohost.com)
  • Construction of a 3-Mb contig and partial transcript map of the central region of mouse chromosome 11. (stanford.edu)
  • Genetic mapping of 21 genes on mouse chromosome 11 reveals disruptions in linkage conservation with human chromosome 5. (stanford.edu)
  • The presence of recombination hot and cold spots has a bearing on efforts to map disease genes and for the understanding of the biological properties of chromosome location. (els.net)
  • Relationship between the male (mcM) and female (fcM) genetic maps for chromosome 22. (els.net)
  • A high-density YAC contig map of human chromosome 22. (bath.ac.uk)
  • A 6.5-Mb yeast artificial chromosome contig incorporating 33 DNA markers on the human X chromosome at Xq22. (bath.ac.uk)
  • A recessive mutation of Arabidopsis designated sas1 (for s odium over a ccumulation in s hoot) that was mapped to the bottom of chromosome III resulted in a two- to sevenfold overaccumulation of Na + in shoots compared with wild-type plants. (plantcell.org)
  • BACs can also be utilized to detect genes or large sequences of interest and then used to map them onto the human chromosome using BAC arrays . (wikipedia.org)
  • A 3-Mb sequence-ready contig map encompassing the multiple disease gene cluster on chromosome 11q13.1-q13.3. (semanticscholar.org)
  • The OAR18q linkage map and human HSA14q transcript map were aligned by genotyping two bovine-hamster whole-genome radiation hybrid panels with the microsatellite markers, as well as with sequences corresponding to HSA 14q genes. (ac.be)
  • A contig is a set of gel readings that are related to one another by overlap of their sequences. (wikipedia.org)
  • The new constraints placed on the orientation of the contigs allows for the placement of highly repeated sequences in the genome. (wikipedia.org)
  • Because of repeats in most genomes, current programs collate sequencing data into a set of assembled sequences, called contigs, instead of a complete genome. (ncku.edu.tw)
  • However, connecting the neighboring contigs with nucleotide sequences requires further efforts. (ncku.edu.tw)
  • have recently proposed a software module, FINISH, to close the gaps between contigs with other contig sequences after scaffolding contigs using an optical map. (ncku.edu.tw)
  • Specifically, it rescales optical map and applies length constraint for selecting the correct contig sequences for gap closure. (ncku.edu.tw)
  • High-quality ESTs were identified, 1,117 in total, from leaf cDNAs and assembled into 502 contigs, comprising 202 consensus sequences and 300 singletons. (nih.gov)
  • Goals include automating methods and optimizing techniques to extract the maximum useful information from maps and sequences. (lsu.edu)
  • At the coarsest resolution are genetic linkage maps, which depict the relative chromosomal locations of DNA markers (genes and other identifiable DNA sequences) by their patterns of inheritance. (lsu.edu)
  • AKwgs3 isolate genome contig sequences, JXXB01 assembly. (vectorbase.org)
  • maculatus3 strain genomic contigs sequences, AmacM1 assembly. (vectorbase.org)
  • CM1001059_A strain genomic contigs sequences, AmelC2 assembly. (vectorbase.org)
  • Arlian strain genomic contigs sequences, SscaA1 assembly. (vectorbase.org)
  • Genetic map, sequences, and annotation of markers used to anchor the physical map below. (usda.gov)
  • The assembly of short reads into contiguous DNA segments (contigs) leads to improved annotations because of the greater information content of longer sequences, including the genomic context of multiple coding regions. (peerj.com)
  • While short contigs are still not anchored and these pseudomolecules have not yet been annotated, they provide long, uninterrupted CS sequences which can be an asset to the wheat community. (usda.gov)
  • Sequence assembly is performed to generate contigs (i.e. overlapping sequences) from short reads generated in the experiment by identifying the overlapping nucleotide sequences belonging to a particular organism. (biomedcentral.com)
  • we have a bacteria sequenced and assebled de novo, the reads were also mapped to a known reference. (biostars.org)
  • I am trying to map the raw reads of a genome back to its assembled genome to generate the pileup. (biostars.org)
  • Reads fully mapped on that reg. (biostars.org)
  • Should Samtools Pileup Be Performed On Uniquely Mapped Reads Or All The Reads? (biostars.org)
  • Dear all, I have assembly my reads with MEGAHIT to get final contigs. (biostars.org)
  • Why map reads back to assembly? (biostars.org)
  • I wanted to know why (and if) is useful to map the reads back to the assembled sequence. (biostars.org)
  • Assembling the reads from such a pair (including, of course, only one copy of the identical sequence) produces a longer contiguous read (contig) of sequenced DNA. (wikipedia.org)
  • This gives additional information about the orientation of contigs constructed from these reads and allows for their assembly into scaffolds in a process called scaffolding. (wikipedia.org)
  • In this sequencing method, a low-resolution map is made prior to sequencing in order to provide a framework to guide the later assembly of the sequence reads of the genome. (wikipedia.org)
  • This exploratory tutorial provides instructions and example data to map short reads to a reference genome with alternate haplotypes. (broadinstitute.org)
  • Instructions are suitable for indexing and mapping reads to GRCh38. (broadinstitute.org)
  • The second workflow takes the processed BAM from the first workflow, makes some adjustments to the reads to maximize their information, and calls variants on the alternate contig. (broadinstitute.org)
  • Venn-diagram numbers in plain format correspond to singleton reads, while numbers in bold correspond to sequencing reads that were assembled into Contigs. (nih.gov)
  • Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. (nature.com)
  • Genomic contigs resulting from de-novo assembling of all 454 genomic reads (fasta format). (hindawi.com)
  • Our approach applies de novo assembly software to experimental reads and so-called pseudoreads and uses the resulting contigs to generate a modified reference sequence. (hindawi.com)
  • This genome sequence is used to map the reads and obtain the final readout of the experiment as the read counts per base pair. (hindawi.com)
  • Most existing assemblers set up contigs mathematically using numerous sequence reads, and each contig is assembled individually. (biomedcentral.com)
  • Correctly set mapq=0 for reads that multi map. (bcgsc.ca)
  • The fruit samples produced 1.13 million ESTs which were assembled into 27,859 contigs with a mean length of 834 base pairs and a mean of 67 reads per contig. (pubmedcentralcanada.ca)
  • 60x coverage) and gap-filled and scaffolded with contigs assembled from Oxford Nanopore Technology long-reads and linkage map results. (usda.gov)
  • Some of HGT genes may be missed because of incompletely contigs assembly, but the 42× coverage of reads were full enough for identification of the existence of these gene segments. (thefishsite.com)
  • Generally, the sequenced reads tend to equally cover the assembly contigs, and eukaryotic contigs were expected to have different reads coverage to those contaminating contigs. (thefishsite.com)
  • Thus, with the help of SOAPaligner ( http://soap.genomics.org.cn/soapaligner.html ), we aligned all the reads to the 14 contigs which showed homologous with the 14 candidate HGT genes. (thefishsite.com)
  • Physical mapping of the regions around D7Mit75 and D7Mit56 has also determined the order of a number of MIT markers that remain unresolved on the Mouse Genome Database (MGD) map. (deepdyve.com)
  • The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. (springer.com)
  • Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement. (springer.com)
  • Recent advances in chickpea genomics have made it possible to not only develop large-scale molecular markers, genetic maps, transcriptomic resources for conducting large-scale and high-throughput marker genotyping but also sequence the genome of this important crop (Varshney et al. (springer.com)
  • Twelve dinucleotide-repeat polymorphic sequence- tagged site (STS) markers that were previously isolated mainly from these YAC and P1 clones were genetically mapped. (elsevier.com)
  • A total of 46 nonpolymorphic STS markers were newly established mainly from the YAC and P1 clone end fragments, and 28 of the 46 nonpolymorphic STSs, as well as the 12 polymorphic STSs, were also mapped physically onto the contig based on STS content analysis of YAC pools and of the P1 and YAC clones. (elsevier.com)
  • Thus, the resulting cloned region, together with densely mapped STS markers on the contig, should help to promote our understanding of this region. (elsevier.com)
  • These markers provided unambiguous anchoring of 129 FPCs and orientation for 30 contigs. (elsevier.com)
  • The map was constructed by hybridizing markers to the library, to a blot of the electrophoretic karyotype, and to a blot of the pulsed-field separation of the Sfi I restriction fragments of the genome. (genetics.org)
  • The map includes 149 fosmids and was constructed using 79 markers, of which 34 were shown to be genes via determination of function or comparison of the DNA sequence to the public databases. (genetics.org)
  • The absolute position of several markers was determined using random breakage mapping. (genetics.org)
  • Of the 61 markers that mapped in the four subregions of the GRR, 9 mapped in the Ph1 gene region. (pnas.org)
  • Seven of the nine Ph1 gene region markers mapped within a 450-kb region on R9 with the same gene order. (pnas.org)
  • The human genetic linkage map is constructed by observing how frequently two markers are inherited together. (lsu.edu)
  • On the genetic map, distances between markers are measured in terms of centimorgans (cM), named after the American geneticist Thomas Hunt Morgan. (lsu.edu)
  • The essence of all genome mapping is to place a collection of molecular markers onto their respective positions on the genome. (wikipedia.org)
  • Genes can be viewed as one special type of genetic markers in the construction of genome maps, and mapped the same way as any other markers. (wikipedia.org)
  • While both maps are a collection of genetic markers and gene loci, genetic maps' distances are based on the genetic linkage information, while physical maps use actual physical distances usually measured in number of base pairs. (wikipedia.org)
  • The first steps of building a genetic map are the development of genetic markers and a mapping population. (wikipedia.org)
  • The quality of the genetic maps is largely dependent upon these factors: the number of genetic markers on the map and the size of the mapping population. (wikipedia.org)
  • The entire process is then repeated by looking at more markers which target that region to map the gene neighbourhood to a higher resolution until a specific causative locus can be identified. (wikipedia.org)
  • Molecular markers from a BAC contig spanning the Rdr1 locus: a tool for marker-assisted selection in roses. (ebscohost.com)
  • From this contig, we developed broadly applicable simple sequence repeat (SSR) markers tightly linked to Rdr1, which are. (ebscohost.com)
  • Database containing BAC libraries, clone fingerprints, markers and contig maps for Hordeum vulgare . (usda.gov)
  • Replaced RiceGenes with information on molecular markers, maps, ontology, comparative mapping among grass species. (usda.gov)
  • ITMI coordinates international efforts in Triticeae linkage and physical mapping, ESTs and bioinformatics, QTLs, large insert libraries, genetic stocks, functional markers and expression analysis. (usda.gov)
  • Barleymap was designed to search the position of barley genetic markers on the Barley Physical Map (IBSC) and the POPSEQ map (Mascher et al. (usda.gov)
  • 2. How important is genome sequencing in terms of funding priorities (vs. placing cDNAs on the map, completion of the physical map, adding more PCR-based markers to the map, etc. (bio.net)
  • The mapping population data revealed 16 major linkage groups with 520 markers, and 10 quantitative trait loci (QTLs) significantly associated with Taro Leaf Blight disease resistance. (usda.gov)
  • A total of 150 markers common t buffelgrass and sorghum have been mapped to both species covering all sorghum linkage groups (LGs). (usda.gov)
  • The method relies on the use of overlapping clones, referred to as contigs. (oup.com)
  • High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. (springer.com)
  • As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. (springer.com)
  • in top-down sequencing projects, contig refers to the overlapping clones that form a physical map of the genome that is used to guide sequencing and assembly. (wikipedia.org)
  • Contigs can thus refer both to overlapping DNA sequence and to overlapping physical segments (fragments) contained in clones depending on the context. (wikipedia.org)
  • This map identifies the relative positions and overlap of the clones used for sequencing. (wikipedia.org)
  • The contig comprises 16 overlapping YAC clones and 44 overlapping P1 clones. (elsevier.com)
  • As a result, the YAC and P1 clones were assembled into a single contig covering a minimum of 1.5 Mb physically and 2.8 cM genetically with 12 polymorphic and 28 nonpolymorphic STSs within the 8p12-p21 region. (elsevier.com)
  • Furthermore, some BAC clones contained multiple genes, making physical mapping feasible. (nih.gov)
  • The genetic map of buffelgrass (Pennisetum ciliare (L.) Link), a tetraploid forage grass has been developed using cDNA from an apomictic pistil library of the species and genomic clones from a number of other grass species. (usda.gov)
  • Thus, the CES critical region has been mapped and a substantial portion of it cloned in preparation for the isolation of genes in this region. (eurekamag.com)
  • Our physical map and transcript map may be useful for positional cloning of genes in this unusually gene-rich region of the genome. (deepdyve.com)
  • Physical mapping of 3,025 gene loci on 334 single-break deletion lines identified 18 major and 30 minor gene-rich regions (GRRs), accounting for 85% of known genes and encompassing only ≈29% of the genome ( 2 ). (pnas.org)
  • The distance between the genes (map units) are equal to the percentage of crossing-over events that occurs between different alleles. (wikipedia.org)
  • Gene mapping describes the methods used to identify the locus of a gene and the distances between genes. (wikipedia.org)
  • This process is often referred to as " positional cloning ", and it is used extensively in the study of plant species The great advantage of genetic mapping is that it can identify the relative position of genes based solely on their phenotypic effect. (wikipedia.org)
  • A map of the human genome will allow scientist to understand where genes are located so that its function within the human genome can be elucidated. (encyclopedia.com)
  • Gene mapping can provide clinicians with useful information regarding genes that are linked, or segregate closely together. (encyclopedia.com)
  • Scientists use several methods to map genes to the appropriate locations. (encyclopedia.com)
  • A cytogenetic map uses bands produced by a dye that stains chromosomes in a karyotpe and assigns genes to these bands. (encyclopedia.com)
  • A linkage map , also referred to as a genetic map , orders genes along the DNA strand based on recombination frequency. (encyclopedia.com)
  • Linkage mapping involves using two characteristics (and hence their responsible genes), both of which are present in one parent, combined with the frequency in which they occur together in the offspring to construct the map. (encyclopedia.com)
  • Genetic mapping and evaluation of candidate genes for spasmodic, a neurological mouse mutation with abnormal startle response. (stanford.edu)
  • Good review of linkage disequilibrium mapping of disease genes. (els.net)
  • The scientific goal was to map the genes and sequence human DNA. (encyclopedia.com)
  • Physical mapping in sorghum is in progress to identify a contig of BACs that encompasses this region and to identify candidate orthologs for apomixis genes. (usda.gov)
  • Ultimately, only 14 candidate HGT genes were homologous to shrimp genomic contigs (E-values ranged from 0 to 9.00E-21, and identity values ranged from 88.22 per cent to 100 per cent). (thefishsite.com)
  • Genomics: international journal of gene mapping and nucleotide sequencing. (uantwerpen.be)
  • Gene structure of contig 2509 (GADD45). (hindawi.com)
  • By telocentric analysis, the Ph1 gene in hexaploid wheat was genetically mapped 1-5 cM from the centromere on 5BL ( 13 , 14 ). (pnas.org)
  • In tetraploid wheat, the gene was physically mapped between the C-bands 5BL1.5 and 5BL2.1 ( 5 , 15 ). (pnas.org)
  • In gene mapping, any sequence feature that can be faithfully distinguished from the two parents can be used as a genetic marker. (wikipedia.org)
  • Finally, a DNA sequence, strung together, is the most precise type of map in that it contains both coding (gene-containing) and noncoding DNA. (encyclopedia.com)
  • PEST strain gene prediction stable identifier mapping for ncRNAs from AgamP3.8 to AgamP4.1. (vectorbase.org)
  • The plan would be that individual groups who have mapped their favorate regions, containing their favorate gene(s), then would send (or take) their physical contigs (cosmids/P1's) to a regional center for sequencing. (bio.net)
  • Morton NE and Collins A (1997) The future of gene mapping. (els.net)
  • Comparisons of the physical and genetic maps of the grass genomes show conservation of gene order and orientation, or synteny ( 5-7 ). (sciencemag.org)
  • A 1.9 Gb draft map of the contigs was assembled and used to identify genuine shrimp gene segments. (thefishsite.com)
  • We have constructed a long-range restriction map of this region using pulsed-field gel electrophoresis and probes to 10 loci (11 probes). (eurekamag.com)
  • Using Type I loci mapping to the IDVGA30-OY3 interval as anchor points, we have constructed a 1.4-Mb bovine BAC contig containing the IDVGA30-OY3 interval. (ac.be)
  • This approach is suitable for calling on ~75% of the non-HLA alternate contigs or ~92% of loci with non-HLA alternate contigs (see table in section 6 ). (broadinstitute.org)
  • From this set of unigenes, 311 (133 SNP and 178 InDel) loci were mapped on the intermated B73 X Mo17 (IBM) high-resolution mapping population. (elsevier.com)
  • By taking advantage of allelic variation revealed by heterologous probes, the positions of corresponding loci on the wheat ( Triticum aestivum ), rice, maize, sugarcane, and Arabidopsis genomes are being interpolated on the sorghum physical map. (plantphysiol.org)
  • Collins A, Frezal J, Teague J and Morton NE (1996) A metric map of humans: 23,500 loci in 850 bands. (els.net)
  • Does anyone know why when doing a de novo assembly of a bacterial isolate and then mapping back t. (biostars.org)
  • Here, we show a contig reordering strategy based on experimental replication profiling (eRP) to recapitulate the bacterial genome structure within draft genomes. (biomedcentral.com)
  • Just layout the contigs in order and use these as 'artificial' scaffolds. (biostars.org)
  • Scaffolds consist of overlapping contigs separated by gaps of known length. (wikipedia.org)
  • The remaining gaps between the contigs in the scaffolds can then be sequenced by a variety of methods, including PCR amplification followed by sequencing (for smaller gaps) and BAC cloning methods followed by sequencing for larger gaps. (wikipedia.org)
  • AGP (v2.0) file relating contigs to scaffolds for the Anopheles gambiae Pimperena strain, AgamS1 assembly. (vectorbase.org)
  • AGP (v2.0) file relating contigs to scaffolds for the Sarcoptes scabiei Arlian strain, SscaA1 assembly. (vectorbase.org)
  • Scaffolds were validated by BioNano optical mapping, and ordered and oriented using linkage and pan-genome marker data. (maizegdb.org)
  • B73 RefGen_v4 assembly utilized a new approach that relied on PacBio Single Molecule Real Time (SMRT) sequencing at Cold Spring Harbor to a depth of 60X coverage with scaffolds created via the assistance of whole genome restriction mapping (aka Optical Mapping). (maizegdb.org)
  • Gaps often remain, and a scaffold-consisting of contigs and gaps-that covers the map region is often the first result. (wikipedia.org)
  • The gaps between contigs can be closed by various methods outlined below. (wikipedia.org)
  • In addition, it uses an advanced graph search algorithm to facilitate estimating the number of repeat copies within gaps between contigs. (ncku.edu.tw)
  • Gaps between contigs are indicated by runs of 1000 N's. (maizegdb.org)
  • The real problem is in closing gaps between shotgun generated contigs not in error correction. (bio.net)
  • Return to Contiguous (contig) map . (webref.org)
  • A contig (from contiguous) is a set of overlapping DNA segments that together represent a consensus region of DNA. (wikipedia.org)
  • The gel readings in a contig can be summed to form a contiguous consensus sequence and the length of this sequence is the length of the contig. (wikipedia.org)
  • A sequence contig is a continuous (not contiguous) sequence resulting from the reassembly of the small DNA fragments generated by bottom-up sequencing strategies. (wikipedia.org)
  • Here, a contig still refers to any contiguous stretch of sequence data created by read overlap. (wikipedia.org)
  • How to get sequencing fragment data from an automated sequencer into the computer and assembled into a contiguous sequence (contig) using GCG's SeqMerge, and then how to perform restriction enzyme mapping and compositional analysis on that contig for subcloning and other purposes. (fsu.edu)
  • One common strategy is to use sequence-tagged site (STS) content mapping to detect unique DNA sites in common between BACs. (wikipedia.org)
  • In this paper, we introduce the experimental replication profiling (eRP) arrangement strategy, which analogizes the positional relationship between contigs based on the biological molecular behavior information. (biomedcentral.com)
  • In this study we demonstrate their utility for locating fingerprint contigs (FPCs) to the genetic map. (elsevier.com)
  • It is therefore difficult to establish a genetic map by means of recombination frequencies. (genetics.org)
  • The current resolution of most human genetic map regions is about 10 Mb. (lsu.edu)
  • Researchers begin a genetic map by collecting samples of blood or tissue from family members that carry a prominent disease or trait and family members that don't. (wikipedia.org)
  • The anchoring was validated using high-density diploid and tetraploid genetic maps. (nature.com)
  • Using a high-density RFLP map as a framework, a robust physical map of sorghum is being assembled by integrating hybridization and fingerprint data with comparative data from related taxa such as rice and using new methods to resolve genomic duplications into locus-specific groups. (plantphysiol.org)
  • This will allow for future construction of high-density integrated physical and genetic maps for cotton and other complex polyploid genomes. (g3journal.org)
  • This makes them ideal candidates for construction of high-density genetic maps, which can then be used for marker-based crop improvement and genetic analyses. (g3journal.org)
  • Detailed alignment of the buffelgrass map to the high density map of sorghum (containing approx. (usda.gov)
  • Utilization of the high density map of sorghum as a tool towards isolation of alleles conferring phenotypes unique to other closely related grass species will be discussed. (usda.gov)
  • A physical map of a BAC clone contig covering the entire autosome insertion between ovine MHC Class IIa and IIb. (ebscohost.com)
  • 99.99% accurate sequence using a mapped clone sequencing strategy ( 8 ). (sciencemag.org)
  • Is there any open source assembly softwares that takes in de novo assembly generated contigs and reference genome to produce bigger contigs( reference guided de novo assembly)? (biostars.org)
  • Fine-mapping and construction of a bovine contig spanning the ovine callipyge locus. (ac.be)
  • Analysis of more than 500 backcross and intercross progeny maps the hyh locus to proximal Chr 7, approximately 13 cM centromeric to its originally reported map position. (deepdyve.com)
  • We constructed a BAC contig of about 300 kb spanning the Rdr1 locus for black spot resistance in Rosa multiflora hybrids, using a new BIBAC library from DNA of this species. (ebscohost.com)
  • Teague JW, Collins A and Morton NE (1996) Studies on locus content mapping. (els.net)
  • Is it possible to combine somehow the data from the mapping and the de novo assembly? (biostars.org)
  • I've got contigs from de novo (Spades) assembly (approx 175 contigs of length 200 bp to 11 kb), a. (biostars.org)
  • In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. (springer.com)
  • The assembly of a contig map involves several steps. (wikipedia.org)
  • This first workflow is suitable for calling variants on the primary assembly but is insufficient for capturing variants on the alternate contigs. (broadinstitute.org)
  • OMACC: an Optical-Map-Assisted Contig Connector for improving de novo genome assembly. (ncku.edu.tw)
  • As optical mapping is becoming popular and repeats are the bottleneck of assembly, OMACC should benefit various downstream biological studies via accurately connecting contigs into a more complete genome. (ncku.edu.tw)
  • The assembly was then mapped onto the current genome data. (nih.gov)
  • A descriptive analysis of planarian splice sites was conducted on those Smed454 contigs that mapped univocally to the current genome assembly. (nih.gov)
  • We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). (nature.com)
  • Of the assembly, 95% is contained in only 196 contigs. (nature.com)
  • When Scaffolding with RNA-Seq contigs from a Trans-ABySS assembly, the genic contiguity is greatly improved. (bcgsc.ca)
  • DNA fragment contig assembly (GCG's SeqMerge) and restriction enzyme mapping ( pdf ) ( Lab Report #4 ). (fsu.edu)
  • Here we describe a de novo taro genome assembly and use it to analyze sequence data from a Taro Leaf Blight resistant mapping population. (usda.gov)
  • The haploid assembly was 2.45 Gb total, with a maximum contig length of 38 Mb and scaffold N50 of 317,420 bp. (usda.gov)
  • If the size of a whole human genome is represented by the perimeter of the earth ( ∼4×107m), constructing a whole-genome assembly would be like drawing a world map by using only a 1 m ruler. (deepdyve.com)
  • Hence, the de novo assembly of individual genomes would be a better choice for building a precise map of highly rearranged genomes and for understanding the associated phenotypes. (deepdyve.com)
  • Until now, extensive genetic and physical maps have been required to direct the sequencing effort and sequence assembly for species with large and complex genomes. (ufl.edu)
  • The strategy involves a whole genome shotgun (WGS) sequence assembly including a combination of FISH (fluorescent in situ hybridization), computational sequence assemblers, and whole genome restriction maps (derived from OpGen Incs Whole Genome Mapping technology). (ufl.edu)
  • The alignment results were compared with that of 1,000 randomly selected assembly contigs. (thefishsite.com)
  • The mapping results validated the approach for reliably producing large numbers of both intraspecific and interspecific SNPs aligned to BAC-ends. (g3journal.org)
  • SNPs discovered in the EST contigs used for the Affymetrix Barley1 GeneChip. (usda.gov)
  • An NSF-supported project to discover and map wheat SNPs. (usda.gov)
  • A physical map would help organize these data and provide much useful information about the genetics of the organism. (genetics.org)
  • ETGI coordinates European efforts in barley and wheat physical mapping, sequencing, high resolution genetic mapping, and development of populations for trait mapping with QTLs and association genetics. (usda.gov)
  • Contigs therefore provide the framework for hierarchical sequencing. (wikipedia.org)
  • The FPC anchored map of maize will be useful for map-based cloning, for genome sequencing efforts in maize, and for comparative genomics in grasses. (elsevier.com)
  • Improving the instrumentation and techniques required for mapping and sequencing a major focus of the genome project will increase efficiency and cost- effectiveness. (lsu.edu)
  • More- precise maps are needed to organize systematic sequencing efforts and plan new research directions. (lsu.edu)
  • Therefore, if genome sequencing is performed with appropriate timing, the short-read coverage reflects this copy number gradient, providing information about the contig positions relative to the replication origin and terminus. (biomedcentral.com)
  • Sequencing from reagions already mapped will yield this information directly. (bio.net)
  • Let the mapping and biology be done in individual labs but sequencing is only cost effective if done in centers. (bio.net)
  • Collins A (2000) Mapping in the sequencing era. (els.net)
  • Provides lists of intron-spanning PCR primers derived from mapped ESTs. (usda.gov)
  • He contributed to the first physical map of the Human Genome at Genethon and at Genset Corporation as a member of Daniel Cohen [fr]'s team, collaborating with research teams from Caltech and the Los Alamos National Lab. (wikipedia.org)
  • the emerging rice physical map and assembled sequence will further accelerate progress. (plantphysiol.org)
  • Construction of a BAC library and a physical map of a major QTL for CBB resistance of common bean ( Phaseolus vulgaris L.). Liu, S. Y. (ebscohost.com)
  • Radiation hybrid maps remain useful for connectivity and orientation of sequenced contigs. (els.net)
  • Furthermore, CoMet recovered contigs of more species and was 18 - 39% higher in precision than the compared existing methods in discriminating species from the sample of multiple strains. (biomedcentral.com)
  • The approach proposed with CoMet for binning contigs, improves the precision of binning while characterizing more species in a single metagenomic sample and in a sample containing multiple strains. (biomedcentral.com)
  • CoMet utilizes coverage values and the compositional features of metagenomic contigs. (biomedcentral.com)
  • Binning methods based on both compositional features and coverages of contigs had higher performances than the method which is based only on compositional features of contigs. (biomedcentral.com)
  • so we have contigs built de novo or contigs built according to a close reference. (biostars.org)
  • I would like to work with the de novo contigs but I need to knoe their order. (biostars.org)
  • Or if you have for instance paired-end or mate-pair information you can make an optimised scaffold de novo by mapping the pairs to the contigs and thereby determine the order and distance. (biostars.org)
  • Generate distance estimates between all contigs a single read maps to. (bcgsc.ca)
  • These pseudomolecules were constructed from PacBio contigs anchored on CS BioNano genome maps. (usda.gov)
  • Mapping involves (1) dividing the chromosomes into smaller fragments that can be propagated and characterized and (2) ordering (mapping) them to correspond to their respective locations on the chromosomes. (lsu.edu)
  • Using these methods, various maps of chromosomes can be developed. (encyclopedia.com)
  • These maps are called cytogenetic maps, linkage maps, physical maps, or a DNA sequence map. (encyclopedia.com)
  • I can recommend Mauve Contig Mover, it orders your contigs relative to a reference genome. (biostars.org)
  • The table below lists all contigs included in the genome, listed by GenBank accession, with information regarding where that contig maps to the S288C Reference Genome. (yeastgenome.org)
  • For those who are interested in calling variants on the alternate contigs, we also present a second and a third workflow in section 6 . (broadinstitute.org)
  • In this study, we designed and implemented a new workflow, Coverage and composition based binning of Metagenomes (CoMet), for binning contigs in a single metagenomic sample. (biomedcentral.com)
  • bioinformaticist and software ingeneer at INRA's URGI laboratory (Versailles, France, leaded by Hadi Quesneville) in charge of the development and maintenance of annotation pipelines, physical mapping data management, web services, software maintenance and installation, projects support. (irisa.fr)
  • Human genome maps are constructed on several different scales or levels of resolution. (lsu.edu)
  • A YAC contig map of the human genome. (google.co.uk)
  • 1990) Program description - Centre D'Etude Polymorphisme Humain (CEPH) - collaborative genetic mapping of the human genome. (els.net)
  • 2001) A high resolution radiation hybrid map of the human genome draft sequence. (els.net)
  • Perhaps the first paper to give credible genome map lengths on different map scales. (els.net)
  • In addition, further characterization of the contig suggested that this contig includes a region where genetic recombination occurs frequently. (elsevier.com)
  • however, unlike physical maps, the map distances are related to recombination. (els.net)
  • It is important to integrate genetic and physical or sequence‐based maps to identify regions of elevated or reduced recombination. (els.net)
  • Kosambi DD (1944) The estimation of map distances from recombination values. (els.net)
  • To increase the accuracy of contig connections, we develop OMACC, which carefully takes into account length information in optical maps. (ncku.edu.tw)
  • New option, --max-length, used to remove contigs over the specified threshold. (bcgsc.ca)