Contig Mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Chromosomes, Artificial, Yeast: 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.Sequence Tagged Sites: 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.Physical Chromosome Mapping: 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)Chromosome Walking: 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.Chromosomes, Artificial, Bacterial: 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.Bacteriophage P1: 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.Cosmids: Plasmids containing at least one cos (cohesive-end site) of PHAGE LAMBDA. They are used as cloning vehicles.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Molecular Sequence Data: 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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Documentation: Systematic organization, storage, retrieval, and dissemination of specialized information, especially of a scientific or technical nature (From ALA Glossary of Library and Information Science, 1983). It often involves authenticating or validating information.Gene Library: 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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Radiation Hybrid Mapping: 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.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.IodobenzenesGenetic Linkage: The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.Peptide Mapping: 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.Epitope Mapping: 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.Cloning, Molecular: 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.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Brain Mapping: Imaging techniques used to colocalize sites of brain functions or physiological activity with brain structures.Chromosomes, Plant: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.In Situ Hybridization, Fluorescence: 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.Body Surface Potential Mapping: 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)Software: Sequential operating programs and data which instruct the functioning of a digital computer.Interphase: The interval between two successive CELL DIVISIONS during which the CHROMOSOMES are not individually distinguishable. It is composed of the G phases (G1 PHASE; G0 PHASE; G2 PHASE) and S PHASE (when DNA replication occurs).Microsatellite Repeats: 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).Chromosomes, Bacterial: Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.Chromosomes, Human, Pair 11: A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Amino Acid Sequence: 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.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Epicardial Mapping: 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.DNA, Complementary: 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.Synteny: 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.Chromosomes, Human, Pair 7: A specific pair of GROUP C CHROMOSOMES of the human chromosome classification.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Chromosomes, Human, Pair 3: A specific pair of human chromosomes in group A (CHROMOSOMES, HUMAN, 1-3) of the human chromosome classification.Genes, Plant: The functional hereditary units of PLANTS.Genome, Human: 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.Pedigree: 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.Multigene Family: 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)High-Throughput Nucleotide Sequencing: 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.Repetitive Sequences, Nucleic Acid: 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).DNA Fingerprinting: 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.Chromosomes, Human, Pair 16: A specific pair of GROUP E CHROMOSOMES of the human chromosome classification.Sequence Alignment: 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.Haplotypes: 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.Computational Biology: 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.Models, Genetic: 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.DNA Probes: 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.Intestinal Neoplasms: Tumors or cancer of the INTESTINES.Hybrid Cells: 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.Chromosomes, Human, Pair 12: 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.
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 ...
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.
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 ...
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
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.
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 ...
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...
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.
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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 ...
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. ...
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
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 ...
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.
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 ...
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. . ...
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CCUG <- Blood Dept., PHL, Göteborg; SBL 0071/83. Human blood; Sweden. Type strain. Taxonomy/description (8443). Sequence accession no. whole genome shotgun sequence: LBIB00000000. Murein: A11.20 (8443). (Medium 58, 37°C, anaerobic ...
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. ...
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To explore CR1 distribution in C. porosus, macroarrays were screened with CR1b-derived overgos or a combination of CR1a and CR1b overgos. Comparison of the CR1b- and CR1a/b-probed macroarrays revealed that the CR1a and CR1b subfamilies are not distinguishable in our assay, i.e., virtually no differences in hybridization pattern and intensity were observed when comparing the CR1b and CR1a/CR1b filters (data not shown). It was clear, however, that elements similar to CR1a and b are fairly abundant in C. porosus. Examination of one-quarter of the CR1a/b-probed macroarray (Figure 3A) indicates that 8.9% of clones show hybridization to the CR1a/b overgos while CR1b overgo hybridization to a filter stamped with the contents of a single 384-well plate from the BAC library suggests that 12.8% of clones (49 of 384) are positive for the CR1b overgo (Figure 4). Densitometric analysis of the macroarray reveals that there is a six-fold variation in positive clone hybridization intensity. If the lightest, but ...
Background:The publication of the first draft chicken sequence assembly became available in 2004 and was updated in 2006. However, this does not constitute a definitive and complete sequence of the chicken genome, since the microchromosomes are notably under-represented. In an effort to develop maps for the microchromosomes absent from the chicken genome assembly, we developed radiation hybrid (RH) and genetic maps with markers isolated from sequence currently assigned to chromosome Unknown (chrUn). The chrUn is composed of sequence contigs not assigned to named chromosomes. To identify and map sequence belonging to the microchromosomes we used a comparative mapping strategy, and we focused on the small linkage group E26C13. Results:In total, 139 markers were analysed with the chickRH6 panel, of which 120 were effectively assigned to the E26C13 linkage group, the remainder mapping elsewhere in the genome. The final RH map is composed of 22 framework markers extending over a 245.6 cR distance. ...
Single nucleotide polymorphism (SNP) markers were identified and validated for two stingrays species, Potamotrygon motoro and Potamotrygon falkneri, using double digest restriction-site associated DNA (ddRAD) reads using 454-Roche technology. A total of 226774 reads (65.5Mb) were obtained (mean read length 289±183bp) detecting a total of 5399 contigs (mean contig length: 396±91bp). Mining this data set, a panel of 143 in silico SNPs was selected. Eighty-two of these SNPs were successfully validated and 61 were polymorphic: 14 in P.falkneri, 21 in P.motoro, 3 in both species and 26 fixed for alternative variants in both species, thus being useful for population analyses and hybrid detection.. Keywords ...
Citation: Guo, B., Qin, H., Feng, S., Chen, C.Y., Culbreath, A., Zhang, X., Holbrook Jr, C.C., Ozias-Akins, P., Liang, X. 2011. Genetic Linkage Map will aid the Whole genome Sequence Assembly. American Phytopathological Society Abstracts. 2011 American Phytopathological Society International Plant Protection Congress Joing Meeting in Honolulu, HI on August 6-10, 2011. Interpretive Summary: Technical Abstract: The allotetraploid peanut genome assembly will be a valuable resource to researchers studying polyploidy species, in addition to peanut genome evolution and domestication other than facilitating QTL analysis and the tools for marker-assisted breeding. Therefore, a peanut linkage map will aid genome assembly, acting as an independent resource against which contig assembly can be validated. The objective of this study was to develop a comparative integrated map from two recombinant inbred line populations. A total of 4576 SSR markers from three sources: published SSR markers, newly developed ...
Department of Genetics, Harvard Medical School, Boston, MA, USA.. A method for construction of bacterial artificial chromosome (BAC) contigs from a yeast artificial chromosome (YAC) physical map is described. An approximately 2 Mb contig, consisting of two large BAC contigs linked by a small YAC, has been assembled in the region around 80 cM of Arabidopsis thaliana chromosome 2. Clones from this contig will facilitate gene isolation in the region and can be used directly as substrates for DNA sequencing.. MeSH Terms ...
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Lasergene Genomics allows you to quickly and easily perform and edit de novo genome assemblies from any sequencing platform. Click here to find out more!
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DNA Baser is an affordable alternative for assembly of DNA sequences and generation of contigs. File formats supported are abi, scf and seq (or FASTA). Chromatograms of the assembled sequences are displayed in a synchronized format with the generated contig. Ambiguous bases in the contig are highlighted and corrections are suggested by DNABaser based on Quality Values of the trace files. Minimum input from the user required. Editing of ambiguous bases, including insertion and deletion, is possible. The settings of the assembly engine can be adjusted by the user. The user can personalize the appearance of chromatograms, nucleotides, background. The Quality Values of the trace files are displayed above chromatograms, so that the user can easily decide on the corrections in the final contig. Original chromatogram files are automatically trimmed based on Quality Values. The contig is automatically saved in FASTA format, in the same directory with the original trace files. By using a built-up ...
DNA sequence chromatograms are interpreted to produce nucleotide sequences (basecalling) and corresponding base call quality estimates but whilst these derived views are more commonly used, the traces remain the ultimate reference source for any queries about that particular sequencing reaction. All commonly used sequence assembly packages (for example Bonfield at al, 1995), include proprietary trace browsers to help the user (finisher) distinguish poor quality data from good and so work backwards to recreate a representation of the original sequence. Furthermore, in regions with either trace artifacts specific to a particular sequencing chemistry, or general background contamination, an experienced finisher might be able to diagnose correctly the underlying problem and provide a better basecall when provided with a suitable view of the original trace. As with contig assembly, trace availability can increase the success rate of STS development from ESTs by enabling an optimal estimation of the ...
Thanks for the plug of our paper, and taking time to give us feedback. I have enjoyed the discussion this kicked up. Its a nice benefit of releasing pre-prints. I think weve covered most of whats below on twitter, but Im putting a summary here.. First, 2nd gen costs werent included in the original arXiv version of this paper, nor were 2nd gen assemblies. The primary intent of our paper is to show whats algorithmically possible with PacBio sequencing, and how long reads significantly drive down the cost of genome *finishing* and enable 1-contig assemblies. Thanks for you kind words on that, main part, of the paper! From our results, I dont think there is any debate that PacBio is much, much cheaper for genome finishing than any other approach, and is capable of some pretty cool stuff.. Adding the comparisons to 2nd gen assemblies was recently added for context; essentially, what assembly does each platform produce, at what price. You took particular exception to our $300 figure for a ...
Shotgun sequencing is the dominant method for genome sequencing in the post-genomic world. The approach, in a nutshell, involves sequencing random fragments of the genome, then assembling those fragments based on sequence overlaps and mate-pair information. You can learn much more about the method here. The shotgun method has benefits in that you do not need to know much about the genetics of the organism whose genome you plan to sequence (of course, the more you know, the easier the process). The main drawback of the method, however, is that it is extremely labor intensive (involving many intermediate steps) and costs an arm and a leg to sequence a eukaryotic genome with good coverage. The quality of a genome sequencing project is defined by how much "coverage" we have of the entire genome. The modern standard is 6-10x coverage. This means that, on average, each nucleotide is sequenced 6-10 times. The higher the coverage, the more confident we are in our nucleotide calls and the higher the ...
Vol 15: The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms.. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
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The constant regions are gBlocks® Gene Fragments and undergo size verification by capillary electrophoresis and sequence verification by mass spectrometry. The variable regions cannot currently receive complete analysis (using NGS, which would be needed for this analysis, would be cost prohibitive). We rely on a validated process that we have experimentally confirmed by NGS that ensures ,80% of DNA species are present in the final material shipped ...
We present here the draft whole-genome shotgun series of an uncultivated strain SNTW101 of species in humans with gastric diseases (1,C4). onto the mouse genome (GRCm38.p1) using Bowtie2 (8) to identify contaminations derived from the host mouse genome. The unmapped reads (4.7 million paired-end reads) were then assembled using Velvet 1/2/10 (9) with optimized parameters […]. Read More ». ...
Incorporating 6 NNK codons corresponds to about 1 billion possible combinations, and 18 N mixed bases will create a pool with 68.7 billion different gene fragments. As the number of variable bases increases, the number of molecules representing a particular sequence decreases. We decided to limit variable regions to 18 mixed bases to give customers the best overall pool of library constructs. Since most functional screens cover 1,000-100,000 recombinant colonies, allowing 18 mixed bases should be adequate for producing meaningful results.. ...
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Under normal circumstances, in un-congested habitats, a bachelor bearded vulture will stake claim to a territory and take-up with a female member of the species; however, with the current surge in population in the Pyrenees, there simply isnt enough available precipitous homesteads for all of the free-roaming males to settle down and raise families of their own. Lacking options, the roving males have developed a new strategy: they have begun to invade the established territories of their rivals - their already attached rivals. The itinerant bachelor invades the home of another male and claims residence with him and his already courted female companion. As might be predicted, the addition of an interloping male into the love nest of an established male-female pair has proven to adversely affect the reproductive success of the mate-pair ...
Under normal circumstances, in un-congested habitats, a bachelor bearded vulture will stake claim to a territory and take-up with a female member of the species; however, with the current surge in population in the Pyrenees, there simply isnt enough available precipitous homesteads for all of the free-roaming males to settle down and raise families of their own. Lacking options, the roving males have developed a new strategy: they have begun to invade the established territories of their rivals - their already attached rivals. The itinerant bachelor invades the home of another male and claims residence with him and his already courted female companion. As might be predicted, the addition of an interloping male into the love nest of an established male-female pair has proven to adversely affect the reproductive success of the mate-pair ...
NCDO <- H.L. Günther <- Techn. Hoogeschool Delft <- C.B. van Niel. Dried American beer yeast. Type strain. Taxonomy/description (1272, 1300, 1317). Sequence accession no. whole genome shotgun sequence: JQBF00000000. Murein: A11.31. (Medium 11, 30°C ...
Cryptographic library offering various cryptographic mechanisms to Apple frameworks. The testing applies to user space and assembler implementations with PAA support ...
Cryptographic library offering various cryptographic mechanisms to Apple frameworks. The testing applies to user space assembler optimized AES ...
gtf1 Not necessarily F1-related, but I have recently learnt that Ricardo Consulting Engineers does engine design and testing for various car companies, and they also build ECU software. (Mostly in 68000 (now named Coldfire) assembler.) ...
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Commentarius de nervis lumbalibus eorumque plexu anatomico-pathologicus. Adiecta est duorum, qui in plexu brachiali majori continentur, nuperque inveniebantur, plexuum minorum descriptio & adumbratio. Cum quatuor tabulis aeneis ...
Title: Physical map construction and physical characterization of channel catfish genome. Name: Xu, Peng. Degree: PhD. Chair: Zhanjiang Liu. Resides: FAA Library. University: Auburn. Location: Auburn, Alabama. Date: 2007. Pages: 111. Keywords: channel catfish genome, gene mapping, genetics. Abstract: Catfish is the major aquaculture species in the United States. To enhance genome studies involving linkage mapping, comparative mapping and linkage map and physical map integration, over 20,000 Bacterial Artificial Chromosome (BAC) end sequences were generated and a BAC-based physical map of the channel catfish (Ictalurus punctatus Rafinesque) genome was constructed using four color fluorescence-based fingerprinting. A total of 25,195 BAC ends were sequenced, generating 20,366 clean BAC end sequences (BES) with an average reading length of 557 bp. The total reading length of 11,414,601 bp represented approximately 1.2% of the catfish genome. Based on this survey, the catfish genome was found to be ...
Mate Pair Library Sequencing enables the generation of libraries with inserts from 2 to 5 kb in size. These long-insert Paired-End libraries are useful for a number of applications, including De NovoSequencing, genome finishing, and structural variant detection. Combining data generated from Mate Pair library sequencing with that from short-insert paired-end reads provides a powerful combination of read lengths for maximal genomic sequencing coverage across the genome. Following DNA fragmentation, 2-5 Kb fragments are end-repaired with biotin labeled dNTPs. The DNA fragments are circularized, and non-circularized DNA is removed by digestion. Circular DNA is fragmented and fragments biotin labels (corresponding to the ends of the original DNA ligated together) are affinity purified. Purified fragments are end-repaired and ligated to Illumina Paired-End sequencing adapters. Additional sequences complementary to the flow cell oligonucleotides are added to the adapter sequence with tailed PCR ...
Strategies for assembling large, complex genomes have evolved to include a combination of whole-genome shotgun sequencing and hierarchal map-assisted sequencing. Whole-genome maps of all types can aid genome assemblies, generally starting with low-resolution cytogenetic maps and ending with the highest resolution of sequence. Fingerprint clone maps are based upon complete restriction enzyme digests of clones representative of the target genome, and ultimately comprise a near-contiguous path of clones across the genome. Such clone-based maps are used to validate sequence assembly order, supply long-range linking information for assembled sequences, anchor sequences to the genetic map and provide templates for closing gaps. Fingerprint maps are also a critical resource for subsequent functional genomic studies, because they provide a redundant and ordered sampling of the genome with clones. In an accompanying paper we describe the draft genome sequence of the chicken, Gallus gallus, the first ...
Manual curation resolved these bifurcations and reduced the number of Citrobacter contigs from ∼1,400 to 10 (the largest curated contig is 2.55 Mb) (Fig. 3B). The final contigs are generally syntenous with the Citrobacter 30_2 strain draft genome (Broad Institute, Cambridge, MA) and the complete Citrobacter koseri ATCC BAA-895 genome (Washington University, St. Louis, MO). Consequently, the fragments were oriented and ordered by reference to the C. koseri genome to generate a final genome representation for the dominant strain, UC1CIT-i (Table S6 in Dataset S2). Of the ten genome gaps, eight are the rRNA-encoding regions that could not be resolved, one is within a prophage, and one is in the intergenic region between genes on contig ends that are adjacent in both isolate genomes.. Citrobacter species are facultative anaerobes from the family Enterobacteriaceae and are commonly found as commensals within the mammalian intestinal tract. Like Serratia, they have been frequently documented as ...
8-base recognition sites will yield pieces 64,000 bases long. Since hundreds of different restriction enzymes have been characterized, DNA can be cut into many different small fragments. Physical Maps Different types of physical maps vary in their degree of resolution. The lowest- resolution physical map is the chromosomal (sometimes called cytogenetic) map, which is based on the distinctive banding patterns observed by light microscopy of stained chromosomes. A cDNA map shows the locations of expressed DNA regions (exons) on the chromosomal map. The more detailed cosmid contig map depicts the order of overlapping DNA fragments spanning the genome. A macrorestriction map describes the order and distance between enzyme cutting (cleavage) sites. The highest- resolution physical map is the complete elucidation of the DNA base- pair sequence of each chromosome in the human genome. Physical maps are described in greater detail below. Low-Resolution Physical Mapping Chromosomal map. In a chromosomal ...
OPPORTUNITY TO PROPOSE ORGANISMS FOR BAC LIBRARY CONSTRUCTION Release Date: December 19, 2001 NOTICE: NOT-HG-02-004 National Human Genome Research Institute Annual Submission Dates: February 10, June 10 and October 10 Over the past several years, the bacterial artificial chromosome (BAC) has emerged as the vector system of choice for the construction of the large- insert chromosomal DNA libraries that are needed in genomic studies. Because BAC clones are relatively large and appear to faithfully represent an organisms genome, the BAC system will also be the vehicle of choice for the isolation of targeted regions of genomic DNA from additional organisms being used in specific biological studies, a variety of mouse strains, and even from individual humans. With the increasing interest in genomic approaches to biological research, the demand for new BAC libraries is expected to increase rapidly in the next several years. To meet the need to increase the number of available BAC libraries, NHGRI, ...
Sequence assembly software http://www.phrap.org. Topic 4: Gene Characterization:. 4-1 P. Carninci, et. al. Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-lenght cDNA libraries for rapid discovery of new genes. Genome Research 2000. 10(10):1617-30. 4-2 M. Stapleton, et. al. The Drosophila gene collection: Identification of putative full length cDNAs for 70% of D. melanogaster genes. Genome Research 2002. 12(8):1294-00.. 4-3 M. Zhang. Computational prediction of eukaryotic protein-coding genes. Nat Rev Genetics 2002. 3(9):698-709.. 4-4 P. Flicek. Gene prediction: compare and CONTRAST. Genome Biology 2007. 8(12):233. 4-5 S. Maas & A. Rich. Changing genetic information through RNA editing. BioEssays 2000. 22(9):790-802. 4-6 F. Perler. A natural example of protein trans-splicing. Trends Biochem Sci 1999. 24(6):209-11.. 4-7 RB Stoughton. Applications of DNA microarrays in biology. Annu Rev Biochem, Jan 2005; 74: 53-82.. 4-8 F Bier et al. DNA microarrays.Adv Biochem ...
Motivation Reproducing the results from a scientific paper can be challenging due to the absence of data and the computational tools required for their analysis. In addition, details relating to the procedures used to obtain the published results can be difficult to discern due to the use of natural language when reporting how experiments have been performed. The Investigation/Study/Assay (ISA), Nanopublications (NP), and Research Objects (RO) models are conceptual data modelling frameworks that can structure such information from scientific papers. Computational workflow platforms can also be used to reproduce analyses of data in a principled manner. We assessed the extent by which ISA, NP, and RO models, together with the Galaxy workflow system, can capture the experimental processes and reproduce the findings of a previously published paper reporting on the development of SOAPdenovo2, a de novo genome assembler. Results Executable workflows were developed using Galaxy, which reproduced results that
Large Venue. The DLP Projector report does the thorough study of the key industry players to understand their business strategies, annual revenue, company profile and their contribution to the global DLP Projector market share. Diverse factors of the DLP Projector industry like the supply chain scenario, industry standards, import/export details are also mentioned in Global DLP Projector Market 2017 report.. Key Highlights of the DLP Projector Market:. A Clear understanding of the DLP Projector market based on growth, constraints, opportunities, feasibility study.. Concise DLP Projector Market study based on major geographical regions.. Analysis of evolving market segments as well as a complete study of existing DLP Projector market segments.. Discover More About Report Here: http://qyresearch.us/report/global-dlp-projector-market-2017/56032/. Furthermore, distinct aspects of DLP Projector market like the technological development, economic factors, opportunities and threats to the growth of DLP ...
One curious aspect of Smalleys comments is his stated replication time for a billion-atom "nanobot": one second. To obtain this blindingly fast replication speed, he adopts a 1 GHz atomic placement frequency approximately one atom positioned every nanosecond. But Drexlers Nanosystems, the canonical textbook in this field, proposed a 1 MHz atomic placement frequency for mature molecular assembler systems with a corresponding replication time of ~103 seconds [4, section 14.3] figures that are commonly adopted in the supporting literature [17]. Other proposals assume replication times up to ~105 seconds (~28 hours) for earlier and more primitive molecular assembler systems [18, 19]. Smalleys proposal of a one second replication time thus appears inconsistent with the extant literature, permitting him erroneously to extrapolate the replicative manufacture of a population of ~1018 nanorobots in just 60 seconds. This in turn leads to a rather obvious fallacy: Allowing ~500 zJ/bond and 1 bond/atom ...
The genomics era has produced an arsenal of resources from sequenced organisms allowing researchers to target species that do not have comparable mapping and sequence information. These new non-model organisms offer unique opportunities to examine environmental effects on genomic patterns and processes. Here we use comparative mapping as a first step in characterizing the genome organization of a novel animal model, the white-throated sparrow (Zonotrichia albicollis), which occurs as white or tan morphs that exhibit alternative behaviors and physiology. Morph is determined by the presence or absence of a complex chromosomal rearrangement. This species is an ideal model for behavioral genomics because the association between genotype and phenotype is absolute, making it possible to identify the genomic bases of phenotypic variation. We initiated a genomic study in this species by characterizing the white-throated sparrow BAC library via filter hybridization with overgo probes designed for the chicken,
Next-generation sequencing (NGS) technologies offer the opportunity for population genomic study of non-model organisms sampled in the wild. The transcriptome is a convenient and popular target for such purposes. However, designing genetic markers from NGS transcriptome data requires assembling gene-coding sequences out of short reads. This is a complex task owing to gene duplications, genetic polymorphism, alternative splicing and transcription noise. Typical assembling programmes return thousands of predicted contigs, whose connection to the species true gene content is unclear, and from which SNP definition is uneasy. Here, the transcriptomes of five diverse non-model animal species (hare, turtle, ant, oyster and tunicate) were assembled from newly generated 454 and Illumina sequence reads. In two species for which a reference genome is available, a new procedure was introduced to annotate each predicted contig as either a full-length cDNA, fragment, chimera, allele, paralogue, genomic ...
Next generation sequencing technologies have revolutionized molecular biology by making whole genome sequencing projects possible for any species. Low coverage whole genome shotgun sequencing has proven a valuable approach for rapid and easy acquisition of a large amount of sequence data at relatively low cost. Low coverage data is useful for marker acquisition as well as the assembly of plastid genomes [20, 21, 31-33]. Despite its power, few examples of the application of NGS on de novo assembly of plant mitochondrial genomes have been reported. Recently Straub and colleagues [22] attempted to assemble the milkweed mitochondrial genome using Illumina data from unenriched whole genome DNA. The assembly resulted in a partial mitochondrial genome assembly of 115 contigs. Here we demonstrate how 454 data from whole genome DNA library can be used for a complete de novo assembly of the mitochondrial genome of Daucus carota. Adequate coverage, sufficient read length, and application of a ...
The availability and throughput of next generation sequencing technologies has enabled the rapid and efficient sequencing of transcriptomes for model and non-model species. The majority of de novo transcriptome assemblies in non-model organisms have in the past been produced using the long reads (300-600 bp) generated using Roche 454 [24]. With the recent developments in sequencing technology, short read sequencers (90-400 bp), such as Illumina and Ion Torrent, are starting to be more commonly used for the generation of large next generation sequencing data sets, as the costs are much lower for the same output [25]. Consequently, the use of short read sequencers to generate de novo transcriptome assemblies for non-model organisms may lead to a more complete gene set for these species at a lower cost. The reliability of de novo transcriptome assemblies generated from short read sequencers, however, needs to be validated to ensure that assemblies are accurate and wont compromise the downstream ...
BOMBYX mori, the domesticated silkworm, is one of the most genetically well-studied insects, with 246 mutations that have been sorted into 27 linkage groups (LGs) (Banno et al. 2005). Genome projects and related work are underway using B. mori as a model organism for Lepidoptera, the most serious group of agricultural pests (for recent review, see Goldsmith et al. 2004). Large-scale sequencing projects of expressed sequence tags (ESTs) (Mita et al. 2003; Cheng et al. 2004) and whole-genome shotgun (WGS) sequences (Mita et al. 2004; Xia et al. 2004) have been performed, and our knowledge of silkworm genes and genome sequence has dramatically increased. However, basic genome research on this insect is still far behind compared with other model organisms such as Drosophila melanogaster, and assignment of fundamental information such as genome sequences, ESTs, BAC contigs, mutant phenotypes, and chromosomal locations on detailed linkage maps is an urgent priority.. Two preliminary molecular linkage ...
Lench NJ, Telford EA, Andersen SE, Moynihan TP, Robinson PA, Markham AF (Dec 1996). "An EST and STS-based YAC contig map of ... syndrome and Fanconi anemia group C in a 2.6-cM interval and contributes to the fine map of 9q22.3". Genomics. 23 (2): 486-9. ...
1997). "An EST and STS-based YAC contig map of human chromosome 9q22.3". Genomics. 38 (2): 199-205. doi:10.1006/geno.1996.0616 ... 2005). "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. doi:10.1038 ...
"A 7.5 Mb sequence-ready PAC contig and gene expression map of human chromosome 11p13-p14.1". Genome Research. 9 (11): 1074-86. ... The interactive pathway map can be edited at WikiPathways: "GlycolysisGluconeogenesis_WP534". GRCh38: Ensembl release 89: ...
1997). "An EST and STS-based YAC contig map of human chromosome 9q22.3". Genomics. 38 (2): 199-205. doi:10.1006/geno.1996.0616 ... Vera C, Lao J, Hamelberg D, Sung LA (2006). "Mapping the tropomyosin isoform 5 binding site on human erythrocyte tropomodulin: ... 2000). "Tropomodulin-binding site mapped to residues 7-14 at the N-terminal heptad repeats of tropomyosin isoform 5". Arch. ...
1999). "A 500-kb sequence-ready cosmid contig and transcript map of the MEN1 region on 11q13". Genomics. 55 (1): 49-56. doi: ...
"A 500-kb physical map and contig from the Harvey ras-1 gene to the 11p telomere". Genomics. 35 (2): 353-60. doi:10.1006/geno. ...
Brown MG, Fulmek S, Matsumoto K, Cho R, Lyons PA, Levy ER, Scalzo AA, Yokoyama MW (1997). "A 2-Mb YAC contig and physical map ...
This process produces a contig map of the locus and is known as chromosome walking. With the completion of genome sequencing ... have now been identified that can be used as traits for mapping. SNPs are the preferred traits for mapping since they are very ... The screen is carried out by mapping mutants of a biological process until no new genes/gene mutations can be found. Christiane ... Depending on the size of the mapping population, the mutant allele can be narrowed down to a small region (. ...
The Gallus gallus genome was sequenced by Sanger shotgun sequencing and mapped with extensive BAC contig-based physical mapping ... 2004). "A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms". Nature. 432 (7018): 717-722. doi ...
"A 7.5 Mb sequence-ready PAC contig and gene expression map of human chromosome 11p13-p14.1". Genome Res. 9 (11): 1074-86. doi: ... 2007). "Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3 (1): 89. doi: ...
"A 2-Mb sequence-ready contig map and a novel immunoglobulin superfamily gene IGSF4 in the LOH region of chromosome 11q23.2". ...
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. ...
1998). "Integrated YAC contig map of the Prader-Willi/Angelman region on chromosome 15q11-q13 with average STS spacing of 35 kb ...
"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 ). ... "Development and mapping of SSR markers for maize". Plant molecular biology. 48 (5-6): 463-81. PMID 12004892. Gardiner, J; ...
... map to a 15-Mb YAC contig spanning Xq21". Genomics. 40 (1): 123-31. doi:10.1006/geno.1996.4542. PMID 9070928. Bione S, Sala C, ... Philippe C, Cremers FP, Chery M, Bach I, Abbadi N, Ropers HH, Gilgenkrantz S (1993). "Physical mapping of DNA markers in the ...
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. Afterwords ...
"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 2-Mb YAC contig and physical map covering the chromosome 8q12 breakpoint cluster region in pleomorphic adenomas of the ... "Functional proteomics mapping of a human signaling pathway". Genome Res. 14 (7): 1324-32. doi:10.1101/gr.2334104. PMC 442148 . ...
1999). "A 1.4-Mb high-resolution physical map and contig of chromosome segment 11p15.5 and genes in the LOH11A metastasis ... "The mapping of the human 52-kD Ro/SSA autoantigen gene to human chromosome 11, and its polymorphisms". Am J Hum Genet. 52 (1): ...
1999). "A 1.4-Mb high-resolution physical map and contig of chromosome segment 11p15.5 and genes in the LOH11A metastasis ... "The structural gene for the M1 subunit of ribonucleotide reductase maps to chromosome 11, band p15, in human and to chromosome ... The interactive pathway map can be edited at WikiPathways: "FluoropyrimidineActivity_WP1601". Ribonucleotide reductase GRCh38: ...
... 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 ...
... construction of an integrated YAC/PAC contig and a partial transcriptional map in the region of chromosome 2q13". Genomics. 41 ... "Entrez Gene: IL1F8 interleukin 1 family, member 8 (eta)". Nicklin MJ, Weith A, Duff GW (1994). "A physical map of the region ... 2002). "A sequence-based map of the nine genes of the human interleukin-1 cluster". Genomics. 79 (5): 718-25. doi:10.1006/geno. ...
"Construction of a 750-kb bacterial clone contig and restriction map in the region of human chromosome 21 containing the ... If a BAC has an insert of length (l), a concordant mapping will show a fragment of size (l) in the reference genome. If the ... In the case of an insertion or a deletion, mapping of the paired-end is consistent with the reference genome. But the read are ... In case of a deletion, the paired-ends are mapped further away in the reference genome compared to the expected distance (l> µ- ...
... construction of an integrated YAC/PAC contig and a partial transcriptional map in the region of chromosome 2q13". Genomics. 41 ... Nicklin MJ, Barton JL, Nguyen M, FitzGerald MG, Duff GW, Kornman K (May 2002). "A sequence-based map of the nine genes of the ... Nicklin MJ, Weith A, Duff GW (January 1994). "A physical map of the region encompassing the human interleukin-1 alpha, ...
... 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 ...
"An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA", Bioinformatics, 10 (3): 309-317, ... of intervals that represent an interval graph can also be used as a way of assembling contiguous subsequences in DNA mapping. A ...
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- ...
... construction of an integrated YAC/PAC contig and a partial transcriptional map in the region of chromosome 2q13". Genomics. 41 ... Nicklin MJ, Barton JL, Nguyen M, FitzGerald MG, Duff GW, Kornman K (May 2002). "A sequence-based map of the nine genes of the ... "Entrez Gene: IL1F10 interleukin 1 family, member 10 (theta)". Nicklin MJ, Weith A, Duff GW (1994). "A physical map of the ...
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 ...
A 2-Mb YAC contig and physical map of thenatural killer gene complex on mouse chromosome 6. Genomics 1997. 42: 16-25. *CrossRef ... Dissen, E., Ryan, J. C., Seaman, W. E. and Fossum, S., An autosomaldominant locus, Nka, mapping to the Ly-49 region of a rat ... Lange, K., Boehnke, M., Cox, D. R. and Lunetta, K. L., Statistical methods for polyploid radiation hybrid mapping. Genome Res. ... A bovine whole-genome radiation hybrid panel and outline map. Mamm. Genome 2002. 13: 469-474. *CrossRef, ...
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. ...
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 ...
"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 ...
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 ...
... 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, ...
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. ...
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 ...
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 ...
... 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) ...
Contigs and their numbers are shown under the map. A 10 kb scale is shown on the left bottom. ... NSRE1 (top, gray box) and NSRE2 (top, open box) were mapped on the draft sequence of the BAC clone GC_Ba0754I06 along with ... Furthermore, some BAC clones contained multiple genes, making physical mapping feasible.. CONCLUSION: We have constructed a ... In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC ...
... number of contigs, total contig map length, average contig length, and average number of markers per contig. ... d, Contig map. The relative position of markers on BAC contigs are indicated by horizontal lines. Contigs are connected to the ... Although the mapped loci nominally appear to cluster at the two ends of the contig, it is premature to assert that this ... based on the sorghum genetic map and comparative maps of other taxa) that are yet to be mapped to the BACs. ...
GRC Map Contigs. hide. dense. full. Hg18 Diff. hide. dense. squish. pack. full. Hg38 Diff. hide. dense. squish. pack. full. Hi ...
GRC Map Contigs. hide. dense. full. Hg18 Diff. hide. dense. squish. pack. full. Hg38 Diff. hide. dense. squish. pack. full. Hi ...
C) BAC contig of R9 with location of markers from the physical map. (D) Location of marker genes in BAC clones mapped on wheat ... Genetic map of wheat chromosome 5BL spanning abc706 and mwg914. (A) Wheat genes, which have been placed on the map by their ... 1986) Location of the Ph1 locus in the metaphase chromosome map and the linkage map of the 5Bq arm of wheat. Can J Genet Cytol ... and 5BL-11 allowed identification of mapped markers at the corresponding BAC contig of rice R9 and in turn at the BAC contig of ...
Optical mapping also supported the contig ordering derived for 2010EL-1786. For all remaining isolates, Illumina-supplemented, ... were mapped to the Newbler contigs by using CLC Genomics Workbench version 4.5 (www.clcbio.com/index.php?id=1042) and yielded ... Newbler-assembled contigs were prepared as pseudogenomes by first linking contigs with a linker sequence containing stop codons ... Next-generation sequence average coverage and number of mapped reads for Vibrio cholerae isolates from Haiti, Asia, and Africa ...
Interspecific linkage mapping of candidate SNPs and anchoring of contigs. From the random and nonrandom (selected for ... TBh104B19r in the same mapping position. The accuracy of mapping BES-associated SNPs makes it possible to utilize SNP mapping ... 2009 BAC-end sequence-based SNPs and bin mapping for rapid integration of physical and genetic maps in apple. Genomics 93: 282- ... Integrating genetic maps with quantitative trait loci (QTL) mapping will allow for utilization of BAC resources for QTL cloning ...
  • 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)
  • 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)
  • 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)
  • These data were used to explore the functional annotation of 45,187 fully annotated contigs. (plos.org)
  • We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. (ucsf.edu)
  • 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)
  • By telocentric analysis, the Ph1 gene in hexaploid wheat was genetically mapped 1-5 cM from the centromere on 5BL ( 13 , 14 ). (pnas.org)
  • To increase the accuracy of contig connections, we develop OMACC, which carefully takes into account length information in optical maps. (ncku.edu.tw)
  • Radiation hybrid maps remain useful for connectivity and orientation of sequenced contigs. (els.net)
  • Both physical maps and diversity maps suggest interesting features that may be integrally related to the chromosomal context of DNA-progress in cytology promises to provide a means to elucidate such relationships. (plantphysiol.org)
  • Construction and characterization of a highly stable human:rodent monochromosomal hybrid panel for genetic complementation and genome mapping studies. (bath.ac.uk)
  • 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)
  • However, alternative methods, such as the construction of partial maps and combination of pedigree and marker information, have also proved useful in identifying marker/trait associations. (science20.com)