Contig Mapping
Chromosome Mapping
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
Bacteriophage P1
Cosmids
Genetic Markers
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
Expressed Sequence Tags
Gene Library
Base 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
Genomic Library
Genetic Linkage
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
Cloning, Molecular
Brain Mapping
Chromosomes, Plant
In Situ Hybridization, Fluorescence
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
Genome
Microsatellite Repeats
Chromosomes, Bacterial
Chromosomes, Human, Pair 11
Amino Acid Sequence
Algorithms
Epicardial Mapping
DNA, Complementary
Synteny
Chromosomes, Human, Pair 7
Chromosomes, Human, Pair 3
Genome, Human
Pedigree
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
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
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
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.
Hybrid Cells
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)
XPA
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. ...
Contig
Contigs therefore provide the framework for hierarchical sequencing. The assembly of a contig map involves several steps. First ... and a scaffold-consisting of contigs and gaps-that covers the map region is often the first result. The gaps between contigs ... Contig can also refer to the overlapping clones that form a physical map of a chromosome when the top-down or hierarchical ... If gaps between contigs remain after STS landmark mapping and restriction fingerprinting have been performed, the sequencing of ...
Laurent Susini
1995). "A YAC contig map of the human genome". Nature. 377 (6547 Suppl): 175-297. doi:10.1038/377175a0 (inactive 31 July 2022 ... "A YAC contig map of the human genome. Nature 1995 Sep; 377(6547 Suppl):175-297. Cited 446 times according to Google Scholar ... He contributed to the first physical map of the Human Genome at Genethon and at Genset Corporation as a member of Daniel Cohen ... Mapping the whole human genome by fingerprinting yeast artificial chromosomes. Cell. 1992 Sep 18;70(6):1059-68. Cited 248 times ...
BAAT
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. Bibcode: ...
Gene mapping
By this approach, physical map contigs can be "anchored" onto a genetic map. The clones used in the physical map contigs can ... There are two distinctive types of "maps" used in the field of genome mapping: genetic maps and physical maps. While both maps ... The two factors are interlinked, as a larger mapping population could increase the "resolution" of the map and prevent the map ... This type of mapping is more accurate than genetic maps. In the early 1950s the prevailing view was that the genes in a ...
E3 binding protein
"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: ...
Tropomodulin 1
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. ...
HRAS
"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. ...
NKG2D
May 1997). "A 2-Mb YAC contig and physical map of the natural killer gene complex on mouse chromosome 6". Genomics. 42 (1): 16- ...
Plant genome assembly
... the physical maps were constructed. The physical maps were integrated together with genetic maps to identify contig positions ... The small pieces are then assembled into contigs by overlapping them. Next, using the map from the first step the contigs are ... The assembly was then polished with the help of Illumina paired-end reads by mapping them to the contigs using BWA-MEM. By ... For Oryza sativa a total of 3,401 mapped clones in a minimum tiling path were selected from the physical map and assembled. One ...
Genetic screen
This process produces a contig map of the locus and is known as chromosome walking. With the completion of genome sequencing ... SNPs are the preferred traits for mapping since they are very frequent, on the order of one difference per 1000 base pairs, ... Depending on the size of the mapping population, the mutant allele can be narrowed down to a small region (. ... Classical geneticists would have used phenotypic traits to map the new mutant alleles. With the advent of genomic sequences for ...
Chicken as biological research model
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. ...
EIF3M
"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: ...
Denaturation mapping
These profiles can be compared to results of an actual denaturation experiment to map the contigs. To this end, more recently ... Denaturation Mapping is a form of optical mapping, first described in 1966. It is used to characterize DNA molecules without ... 1966)."A denaturation map of the lamda phage DNA molecule determined by electron microscopy". Journal of Molecular Biology 18: ... It was not uncommon to ribosomal DNA and compare the resulting maps of related organisms not unlike 16s rRNA identification ...
NRXN2
1999). "A 500-kb sequence-ready cosmid contig and transcript map of the MEN1 region on 11q13". Genomics. 55 (1): 49-56. doi: ...
Cell adhesion molecule 1
"A 2-Mb sequence-ready contig map and a novel immunoglobulin superfamily gene IGSF4 in the LOH region of chromosome 11q23.2". ...
LRRC48
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. ...
PAR1 (gene)
1998). "Integrated YAC contig map of the Prader-Willi/Angelman region on chromosome 15q11-q13 with average STS spacing of 35 kb ...
Bx1 benzoxazin1
"Anchoring 9,371 maize expressed sequence tagged unigenes to the bacterial artificial chromosome contig map by two-dimensional ... 1997 ). Mapping probes: SSR p-umc1022 (Sharopova et al. 2002 ); Overgo (physical map probe) PCO06449 (Gardiner et al. 2004 ). ... 2011 ). Genetic mapping using recombinant inbred lines derived from maize inbred lines B73 and Mo17 showed that a 3.9 kb cis- ... "Development and mapping of SSR markers for maize". Plant Molecular Biology. 48 (5-6): 463-81. doi:10.1023/a:1014868625533. PMID ...
DIAPH2
... 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 ...
SPAdes (software)
Stage 4: contig construction. SPAdes outputs contigs and allows to map reads back to their positions in the assembly graph ... SOAPdenovo Largest contig: IDBA-UD > SPAdes > > EULER-SR > Velvet= E+V-SC > Velvet-SC > SOAPdenovo Mapped genome (%): SPAdes > ... If P is a non-branching path (h-path), then SPAdes maps every edge in P to an edge projection in Q and removes P from the graph ... dipSPAdes constructs longer contigs by taking advantage of divergence between haplomes in repetitive genome regions. Afterwards ...
Bacterial artificial chromosome
"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 ...
TRIM21
Bepler G, O'briant KC, Kim YC, Schreiber G, Pitterle DM (January 1999). "A 1.4-Mb high-resolution physical map and contig of ... Frank MB, Itoh K, Fujisaku A, Pontarotti P, Mattei MG, Neas BR (January 1993). "The mapping of the human 52-kD Ro/SSA ...
PLAG1
Kas K, Röijer E, Voz M, Meyen E, Stenman G, Van de Ven WJ (Nov 1997). "A 2-Mb YAC contig and physical map covering the ... "Functional proteomics mapping of a human signaling pathway". Genome Res. 14 (7): 1324-32. doi:10.1101/gr.2334104. PMC 442148. ...
RRM1
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: ...
Interleukin 37
... 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, ...
IL36B
... 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. ...
End-sequence profiling
"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- ...
IL36G
... 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, ...
IL36A
... 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: IL1F6 interleukin 1 family, member 6 (epsilon)". Nicklin MJ, Weith A, Duff GW (January 1994). "A physical map of ...
Gamma-aminobutyric acid receptor subunit gamma-2
Russek SJ, Farb DH (October 1994). "Mapping of the beta 2 subunit gene (GABRB2) to microdissected human chromosome 5q34-q35 ... and gamma 2 to a YAC contig of 5q33". European Journal of Human Genetics. 4 (4): 199-204. doi:10.1159/000472199. PMID 8875185. ...
CodonCode Aligner
Features include chromatogram editing, end clipping, and vector trimming, sequence assembly and contig editing, aligning cDNA ... "Equine Multiple Congenital Ocular Anomalies maps to a 4.9 megabase interval on horse chromosome 6". BMC Genet. 9: 88. doi: ... against genomic templates, sequence alignment and editing, alignment of contigs to each other with ClustalW, MUSCLE, or built- ...
Vector NTI
... assemble into contigs Bioinformatics Cloning vector Computational biology Expression vector List of open source bioinformatics ... software Restriction map Vector (molecular biology) Vector DNA "Home". http://biodoc.ist.unomaha.edu/wiki/Vector_NTI[dead link ...
RNA-Seq
Metrics to assess the quality of a de novo assembly include median contig length, number of contigs and N50. Genome guided: ... In each case multiple stages of the embryo were studied, allowing the entire process of development to be mapped on a cell-by- ... The output of genome guided alignment (mapping) tools can be further used by tools such as Cufflinks or StringTie to ... Expression is quantified by counting the number of reads that mapped to each locus in the transcriptome assembly step. ...
2 base encoding
Mapping color-space reads to a color-space reference can properly utilize the two-base encoding rules where only adjacent color ... Quality filtering of the reads can deliver higher raw accuracy reads which when aligned to form color contigs can deliver ... Patent: Reagents,Methods and Libraries for Bead-Based Sequencing Article: A high-resolution, nucleosome position map of C. ...
Third-generation sequencing
There was uniform mapping of reads to genome; at least one read mapped to >88% of the genome. The relatively long reads allowed ... Longer patterns of methylation are often lost because smaller contigs still need to be assembled. Transcriptomics is the study ...
OFD1
Brzustowicz LM, Farrell S, Khan MB, Weksberg R (1999). "Mapping of a new SGBS locus to chromosome Xp22 in a family with a ... 1995). "A 6-Mb YAC contig in Xp22.1-p22.2 spanning the DXS69E, XE59, GLRA2, PIGA, GRPR, CALB3, and PHKA2 genes". Genomics. 25 ( ... maps to Xp22.2-Xp22.3". Hum Mol Genet. 6 (7): 1163-7. doi:10.1093/hmg/6.7.1163. PMID 9215688. "Entrez Gene: OFD1 oral-facial- ... a novel human cDNA mapping to Xp22 and encoding a protein containing coiled-coil alpha-helical domains". Genomics. 51 (2): 243- ...
Single-cell DNA template strand sequencing
... which ultimately helps resolve the placement of contigs. Contigs present in the same chromosome will exhibit the same ... and other large chromosomal abnormalities are likely to share this mapping resolution (if breakpoint fine-mapping is performed ... Misoriented contigs are present where strand inheritance changes from one homozygous state to the other (ex. WW to CC, or CC to ... Scaffolds, successive contigs intersected by a gap, can be localized in the same manner. The same principle of using strand ...
ZNRD1
... establishment of a cosmid contig and identification of a new gene cluster within 37 kb of sequence". Genomics. 37 (3): 316-26. ... "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. Bibcode:2005Natur. ...
UGENE
Sequence Alignment/Map(SAM) (.sam), binary version of SAM (.bam), ACE (.ace), FASTQ (.fastq) Phylogenetic trees: Newick (.nwk ... and edit phylogenetic trees Combine various algorithms into custom workflows with UGENE Workflow Designer Contigs assembly with ... results in a nucleic acid sequence with UGENE Query Designer PCR in silico for primer designing and mapping Spade de novo ... for PCR primer design Plasmid construction and annotation Cloning in silico by designing of cloning vectors Genome mapping of ...
HSPB8
Irobi J, Tissir F, De Jonghe P, De Vriendt E, Van Broeckhoven C, Timmerman V, Beuten J (2000). "A clone contig of 12q24.3 ... mapping of a locus to chromosome 12q24". Hum. Mol. Genet. 5 (7): 1065-9. doi:10.1093/hmg/5.7.1065. PMID 8817349. ...
Outline of genetics
... chromosome chromosomal translocation cloning congenital disorder contig craniosynostosis cystic fibrosis cytogenetic map ... gene library gene mapping gene pool gene therapy gene transfer genetic code ATGC genetic counseling genetic linkage genetic map ... karyotype knockout leukemia List of human genetic disorders locus LOD score lymphocyte malformation Gene mapping marker ... sequence nucleus oligo oncogene oncovirus p53 Particulate inheritance theory patent pedigree peptide phenotype physical map ...
CLN5
"Efficient construction of a physical map by fiber-FISH of the CLN5 region: refined assignment and long-range contig covering ... 2007). "Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3 (1): 89. doi: ...
Genomic library
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- ...
Optical mapping
To serve as scaffolds for assembly, assembled sequence contigs can be scanned for restriction sites in silico using known ... high-resolution restriction maps from single, stained molecules of DNA, called "optical maps". By mapping the location of ... Individual optical maps are combined to produce a consensus, genomic optical map. DNA molecules were fixed on molten agarose ... Initially, the optical mapping system has been used to construct whole-genome restriction maps of bacteria, parasites, and ...
DNA sequencing theory
... that both models produced similar results when the number of contigs was substantial, such as in low coverage mapping or ... One of the more frequently used results from this model is the expected number of contigs, given the number of fragments ... Although they focused on the so-called mapping problem, the abstraction to sequencing is much the same. They furnished a number ... The basic ideas of Lander-Waterman theory led to a number of additional results for particular variations in mapping techniques ...
Transcriptomics technologies
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (July 2008). "Mapping and quantifying mammalian transcriptomes by RNA- ... Annotation-based metrics are better assessments of assembly completeness, such as contig reciprocal best hit count. Once ... will accept binary alignment map format read alignments as input. The final outputs of these analyses are gene lists with ... "The Sequence Alignment/Map format and SAMtools". Bioinformatics. 25 (16): 2078-9. doi:10.1093/bioinformatics/btp352. PMC ...
HYAL2
April 1996). "Construction of a 600-kilobase cosmid clone contig and generation of a transcriptional map surrounding the lung ...
De novo transcriptome assembly
In addition to being annotated for GO terms, contigs can also be screened for open reading frames (ORFs) in order to predict ... Prior to the development of transcriptome assembly computer programs, transcriptome data were analyzed primarily by mapping on ... In simulations, Velvet can produce contigs up to 50-kb N50 length using prokaryotic data and 3-kb N50 in mammalian bacterial ... Since a well-resolved reference genome is rarely available, the quality of computer-assembled contigs may be verified either by ...
DNADynamo
... editing and annotating Contig assembly and chromatogram editing including comparison to a reference sequence to identify ... for viewing restriction cut sites in tables and on linear and circular maps. A Subcloning tool for the assembly of constructs ...
Metagenomics
... they were able to generate 6.58 million contigs greater than 500 bp for a total contig length of 10.3 Gb and a N50 length of ... 2018). "Mapping the virome in wild-caught Aedes aegypti from Cairns and Bangkok". Sci Rep. 8 (1): 4690. Bibcode:2018NatSR... ... Misassemblies can also involve the combination of sequences from more than one species into chimeric contigs. There are several ... Metagenomic analysis pipelines use two approaches in the annotation of coding regions in the assembled contigs. The first ...
Ancient DNA
A Map and Status of Ancient Remains - samples from USA no sequence data here. "Unravelling the mummy mystery - using DNA". ... automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly". PeerJ. 9: e11845. doi: ...
CRADD
Horvat S, Medrano JF (1998). "A 500-kb YAC and BAC contig encompassing the high-growth deletion in mouse chromosome 10 and ... "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173-8. Bibcode:2005Natur. ...
HNRPA3
2007). "Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3 (1): 89. doi: ... 1993). "A 1.5-megabase yeast artificial chromosome contig from human chromosome 10q11.2 connecting three genetic loci (RET, ...
MicrobesOnline
The map of a particular pathway and a comparison between two kinds of microbes can be shown in the pathway browser. The enzyme ... having a unique label per contig, (3) preferably gene predictions should be present (in this case, accepted formats include ... The Pathway Browser lets users to navigate the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway maps displaying predicted ... Bates, J. T.; Chivian, D.; Arkin, A. P. (2011). "GLAMM: Genome-Linked Application for Metabolic Maps". Nucleic Acids Research. ...
DNA sequencer
... genome.cshlp.org/content/18/11/1851 Mapping short DNA sequencing reads and calling variants using mapping quality scores. ... compared to the length of a genome therefore the reads must be assembled into longer contigs. The data may also contain errors ... GS Reference Mapper maps short reads to a reference genome, generating a consensus sequence. The software is able to generate ... It uses the MaxMapper algorithm to map the colour space reads. Beckman Coulter (now Danaher) has previously manufactured chain ...
The genome sequence of Drosophila melanogaster
DeCS - Termos Novos
Human hg19 chr12:13,722,953-13,722,953 UCSC Genome Browser v448
Comparative Genomics of Vibrio cholerae from Haiti, Asia, and Africa - Volume 17, Number 11-November 2011 - Emerging Infectious...
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 ...
Human hg19 chr6:32,577,963-32,577,983 UCSC Genome Browser v448
Human hg19 chr2:25,383,722-25,391,559 UCSC Genome Browser v448
Miron LIVNY | University of Wisconsin-Madison, Wisconsin | UW | Department of Computer Sciences | Research profile
Ordering FPC contig sequence pseudomolecules based on the map alignments between optical maps and the in silico maps of the FPC ... FPC gap estimations based on map alignments between optical maps and the in silico maps of FPC contig sequence pseudomolecules ... Using optical contigs to estimate sizes of gaps between adjacent FPC contigs. (A) Restriction map view (box = restriction ... Discordances in the well-aligned map segments between optical maps and the in silico maps of the B73 RefGen_v1 reference ...
PATCH v2 0/6] netfs, afs, ceph: Support folios, at least partially
... contig(mapping, start / PAGE_SIZE, - PAGEVEC_SIZE, pv.pages); - if (pv.nr == 0) - break; + _debug(kill %lx (to %lx), index, ... mapping, ==, mapping); + BUG_ON(xa_is_value(folio)); + ASSERTCMP(folio_file_mapping(folio), ==, mapping); - put_page(page); + ... mapping != mapping); + BUG_ON(folio_file_mapping(folio) != mapping); - if (!afs_dir_check_page(dvnode, page, req-,file_size ... mapping = vnode-,vfs_inode.i_mapping; - struct page *page; + struct folio *folio; pgoff_t end; XA_STATE(xas, &mapping-,i_pages ...
Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities | Communications...
Metagenomic reads were back-mapped to the contigs dataset (bowtie109 v2.3.4.1 with default options), keeping only mapping hits ... The abundance of each MAG was assessed by mapping competitively the reads from the 58 metagenomes against the MAGs contig ... Assemblies from high-quality MAGs were examined visually in Geneious v10.2.4 and contigs that aligned fully to a larger contig ... contig coverage divided by contig length and sequencing depth of the sample, as in Brum et al.105). Next, these 485 "deep-sea" ...
Microorganisms | Free Full-Text | Use of High-Throughput Sequencing and Two RNA Input Methods to Identify Viruses Infecting...
Although the number of contigs mapping to the plant virus database decreased with the subsets, the average contig length was ... Fifty-five assembled contigs, with an average length of 3698 nt, derived from TomDS, mapped with our plant virus database, ... The filtered reads were de novo assembled, and long contigs were mapped by BLASTn against our own plant virus database (Figure ... The presence of divergent viral sequences was investigated by mapping contigs against a custom plant virus protein database ...
Comparative genome analysis of Streptococcus infantarius subsp. infantariusCJ18, an African fermented camel milk isolate with...
Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and...
... we assigned taxonomic labels to each contig of that species against which the largest fraction of the contig mapped with a mean ... We aligned contigs with progressiveMauve [33] (build date Feb 132,015) and used only contigs that spanned the operon completely ... We then blasted these contigs back against all HQ E. rectale genomes, targeting strains of ErEurope with long contigs not ... We considered a contig to come from E. rectale if it mapped with a mean identity score of at least 95% over at least 50% of its ...
Which hg38 file?
Software | Spaz.ca
DeCS - New Terms
DeCS - Termos Novos
DeCS - Termos Novos
Pesquisa | Biblioteca Virtual em Saúde - BRASIL
The final sequence motif map assembly contains three contigs. With an average distance of 9 kb between labels, we detect 22 ... We also use the sequence motif maps to provide scaffolds for de novo assembly of sequencing data. Nanochannel genome mapping ... We describe genome mapping on nanochannel arrays. In this approach, specific sequence motifs in single DNA molecules are ... We obtain accurate, haplotype-resolved, sequence motif maps hundreds of kilobases in length, resulting in a median coverage of ...
Find Research outputs
- The University of Aberdeen Research Portal
Human hg19 chr2:25,383,722-25,391,559 UCSC Genome Browser v448
Human hg19 chr2:25,383,722-25,391,559 UCSC Genome Browser v448
Human hg19 chr2:25,383,722-25,391,559 UCSC Genome Browser v448
![lecture notes:04-30-2010 [Banana Slug Genomics]](data:image/png;base64,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)
lecture notes:04-30-2010 [Banana Slug Genomics]
contig. The between contigs files are for when the reads mapped to different. contigs. Only cases with unique mappings are in ... map-colorspace5. bme235/assemblies/Pog/map-colorspace5 just the mappings of the solid pairs to the 31 contigs made by newbler. ... crossed a contig boundary). Looking at the first line: How many reads support contig 22 following. contig 3? 34K. The contigs ... Order and orient the contigs. Try to do it. Do the contig alignments from the .join file.. (Kevin had already re-done the map- ...
Sinopyrophorinae, a new subfamily of Elateridae (Coleoptera, Elateroidea) with the first record of a luminous click beetle in...
later iterations referred to assembled contigs in the latest iteration); 2) mapped reads were then assembled using SPAdes v3.11 ... Total 38 Gb clean reads were used for assembling 18S and 28S based on the following method: 1) reads were mapped to reference ... 3) tandem contigs were filtered using mereps v2.6 because a huge number of repetitive reads greatly lowers assembly efficiency ...
View FISH image - Sol Genomics Network
Comparison of prokaryotes between Mount Everest and the Mariana Trench | Microbiome | Full Text
... min-contig-len 500 [39]. Clean reads were then mapped to contigs using bbmap.sh (last modified on February 13, 2020) with ... Briefly, reads mapped to genes were normalized by gene length and total mapped number following the formula below:. $$\textrm{ ... After mapping KOs to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway modules, 91% of mapped function modules were ... in which ri and li refer to the reads mapped to gene i and the length of gene i. The significant difference between different ...
Overgo probes on plate 1. - Sol Genomics Network
View of Surveillance of avian influenza viruses in Papua New Guinean poultry, June 2011 to April 2012 | Western Pacific...
Remaining reads were then de novo assembled using the fast-contig mapping mode at the minimum contig length of 200 base pairs; ... Figure 1. Map of Papua New Guinea showing the 14 provinces where sampling was conducted * Click to download Figure 1. jpg, ... Assembled contigs were then subjected to BLASTn search against the National Center for Biotechnology Information (Bethesda, MD ...
January 2019 - Small-Molecule Inhibitors of the MDM2-p53 Protein-Protein Interaction
Computational Genomics Lab | Coscinasterias transcriptome
... soap/starfish.contig.log \ 2, ./starfish_soap/starfish.contig.err # step3: mapping reads SOAPdenovo-Trans-127mer map -s ./ ... Mapping 454 reads over the transcriptome contigs. # Preparing BOWTIE2 target databases (for the transcript contigs) while read ... trimmo.contig.log \ 2, ./starfish_soap_trimmo/starfish_trimmo.contig.err # step3 SOAPdenovo-Trans-127mer map -s ./starfish_soap ... Retrieving best scoring alignments for each contig. # get best HSPs for starfish contigs for TI in newbler trinity_trimmo soap_ ...
Human genome6
- We developed an analysis strategy that resulted, after confirmatory tests, in a YAC contig map reliably covering about 75% of the human genome in 225 contigs having an average size of about ten megabases. (nih.gov)
- A first-generation physical map of the human genome. (nih.gov)
- To facilitate more precise positional mapping and identification of pathogenetically relevant genes, we analysed of human genome contig and sequence databases spanning the deleted regions. (nih.gov)
- GENOMICS 1, 103-106 (1987) EDITORIAL Toward a Complete Map of the Human Genome There are many ways to portray the linear organi- zation of the elements of the chromosomes. (nih.gov)
- In gen- eral, the human genome can be represented in physi- cal maps or in genetic maps. (nih.gov)
- The latter variation can be used to create a reference map of the human genome which for maxi- mal usefulness might have a RFLP marker located each 1 cM, on the average. (nih.gov)
Chromosomes3
- Analyses of rodent-human somatic-cell hybrids, YAC contigs, and FISH of normal or rearranged chromosomes 15 identified duplicated sequences (the END repeats) at or near the breakpoints. (nih.gov)
- Name the chromosomes and contigs that we get as a BLAST hits. (nih.gov)
- At least 1200 expressed genes have been placed on the physical map, i.e., assigned to specific chromosomes and in many instances to spe- cific bands. (nih.gov)
Genes7
- One can query for genes, contigs, change map display options and more. (nih.gov)
- We develop FuSeq, a fast and accurate method to discover fusion genes based on quasi-mapping to quickly map the reads, extract initial candidates from split reads and fusion equivalence classes of mapped reads, and finally apply multiple filters and statistical tests to get the final candidates. (biomedcentral.com)
- In the SR pipeline, fusion candidates are collected from split reads where two different genes share the same read, and each gene has at least k-mer mapped bases. (biomedcentral.com)
- Zoom out several times by clicking on rightmost map and selecting the appropriate option till you can visualize the entire HBB and HBD genes. (nih.gov)
- Multiple known candidate genes and several smaller gene-rich areas mapping to the target regions of chromosome 16 were identified. (nih.gov)
- this can be related to the band map and expressed genes can be related to contigs. (nih.gov)
- Like the map of expressed genes, the individual RFLP markers and the RFLP map as a whole can be related to the band map by somatic cell hybridization and in situ hybridization, and to the contig map, as well. (nih.gov)
Reads10
- More than 600,000 reads produced in a single 454 sequencing run were assembled into approximately 40,000 contigs with five-fold average sequencing coverage. (nih.gov)
- FuSeq consists of two separate pipelines based on mapped read-pairs (MR) and junction split-reads (SR) that are combined in the final step. (biomedcentral.com)
- Instead, it figures out the insert size by mapping paired reads on contigs. (biostars.org)
- It mapped 10000 reads and gave an estimate of just the median insert size as 328. (biostars.org)
- I would suggest you to once again estimate insert size and std deviation using picard tool giving .bam file as input which is generated from estimate_insert_size.pl by mapping reads to contigs. (biostars.org)
- It contains the same tools as the CLC Genomics Workbench, such as mapping of reads to a known reference, de novo assembly, and variant calling. (ethz.ch)
- 48% of the reads mapped. (ucsc.edu)
- It made no sense that 23% of the reads were mapping nowhere. (ucsc.edu)
- The final typing would be performed by incorporating these reads into a shotgun assembly and then scoring each contig as present or absent in a pool. (blogspot.com)
- But, since these reads are primarily for building a physical map (or, in sequence terms driving to larger supercontigs), that may not be fatal. (blogspot.com)
Somatic-cell1
- most of the map created by interspecies somatic cell hybrid- ization and by in situ chromosomal hybridization is of this type (for mapping, however, molecular genetic methods make it unnecessary that the segment of DNA be expressed). (nih.gov)
Sequences1
- There is a possibility that mutations in known sequences, mapped during the efforts to clone the Huntington's disease locus, are responsible for this phenotype. (nih.gov)
Pairs1
- bme235/assemblies/Pog/map-colorspace5 just the mappings of the solid pairs to the 31 contigs made by newbler. (ucsc.edu)
Alignment2
- To address this, we develop FuSeq, a novel fusion detection method utilizing a recent quasi-mapping method for alignment that is substantially faster than traditional alignment methods [ 26 ]. (biomedcentral.com)
- Li H. , Handsaker B. , Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. (nih.gov)
Genetic7
- Genetic mapping and DNA sequence-based analysis of deleted regions on chromosome 16 involved in progression of bladder cancer from occult preneoplastic conditions to invasive disease. (nih.gov)
- Histologic and genetic mapping with 30 hypervariable markers mapped to chromosome 16 were performed on 234 DNA samples of five cystectomy specimens from patients with invasive bladder cancer. (nih.gov)
- Genetic Maps (Linkage Maps) The primary genetic map depicts the location of gene loci (expressed DNA segments) in relation to each other. (nih.gov)
- Variation at the loci in question is essential to genetic mapping. (nih.gov)
- Other compli- cations in relating the genetic map to the physical map are (1) the occurrence of recombination "hot- spots," i.e., inhomogeneity in the distribution of crossovers, and (2) differences in the frequency of crossingover in males and females, this being greater in females in most but not all parts of the genome. (nih.gov)
- The variation in DNA that is the basis of genetic mapping may be reflected in the phenotype, i.e., in disorders such as Huntington's disease or cystic fi- brosis, or in immunologic, electrophoretic, or physio- logic variation, such as ABO blood group, esterase D type, or colorblindness. (nih.gov)
- VNTR (variable number of tandem repeats) recognized by certain restriction enzymes are yet an- other form of polymorphism highly valuable in creat- ing the primary genetic map. (nih.gov)
Markers1
- By typing markers across these pools, a map can be generated. (blogspot.com)
Loci1
- Two NSHHI loci map to the X chromosome (7,8). (nih.gov)
Viewer4
- A set of maps are now available through the NCBI map viewer for 17 organisms. (nih.gov)
- To visualize the BLAST hits on the genome using Map Viewer, click on the 'Genome View' button at the top of the results page, then on the chromosome '11' or the contig link. (nih.gov)
- Go back to the Map Viewer report by clicking the 'back' browser button once. (nih.gov)
- Go back to the Map Viewer report. (nih.gov)
Nucleotide3
- There is an A/T SNP at the nucleotide position 5248232 on NC_000011.9 as shown in the Integrated Maps and GeneView sections. (nih.gov)
- They are mapped to the genome and can be searched by motif, type of nucleotide or amino acid substitution, and location within a splice site or regulatory region. (nih.gov)
- The nucleotide sequence is the ultimate physical map. (nih.gov)
Size1
- How would this help in scaffolding with a program like SSPACE_Standard, which uses insert size to scaffold contigs? (biostars.org)
Read1
- 5000 were not a good read, "invert" if mapped to opposite strands. (ucsc.edu)
Molecular1
- if you can extract high molecular weight DNA from an organism then a HAPPy map should be possible. (blogspot.com)
Regions2
Physical map4
- 19. A BAC clone-based physical map of ovine major histocompatibility complex. (nih.gov)
- A second paper which triggered my current physical map madness is a piece (open access! (blogspot.com)
- The Physical Map The photograph of the high-resolution banded kar- yotype and the idiogram derived therefrom is a basic physica] map and the map at lowest resolution, per- haps 1000 elements at the most. (nih.gov)
- The cDNA Map Another type of physical map is the cDNA map, also called exon map or mRNA map. (nih.gov)
Make2
Reference1
- Studies for creation of a "saturated" RFLP reference map can be done in "'li- braries" of the DNA from a limited number of "com- plete" families: a sibship of eight or more children plus the parents and four grandparents. (nih.gov)
Change2
- lock (Michal) Also, - Separate patch to change type of free_contig_range(nr_pages) to an unsigned long so that it is consistent with other uses of nr_pages. (kernel.org)
- After creating the interface, change alloc_gigantic_page() to call find_alloc_contig_pages() and delete all the supporting code in hugetlb.c. (kernel.org)
Range1
- The alloc_contig_range() interface is used for this purpose today by CMA and gigantic page allocation. (kernel.org)
Structure2
Method1
- HAPPy mapping is a method developed by Simon Dear for physical mapping. (blogspot.com)
Interface1
- Additional features are variant maps, Manhattan plots and a Python scripting interface. (nih.gov)
Options2
Simply1
- Simply follow the naming convention "chromosomeX.contig.embl" where X=1,2,3 etc. (nih.gov)
Variation2
Version1
- The defective gene in tilted mice maps to the syntenic mouse chromosome 5 and may be the mouse version of the human dominant NSHHI gene that our lab recently localized to a region on chromosome 4p that is bounded by the Huntington's disease locus. (nih.gov)
Resolution1
- The number of libraries presumably affects both resolution and confidence in the map. (blogspot.com)
Additional1
- The responsible dn gene maps to mouse chromosome 19 (D19MIT14, 60, and 41), which is syntenic with human chromosome 9q21 and therefore represents an additional potential location for a human NSHHI-related gene (10). (nih.gov)
