• All genes mapped within or near chromosomal locations with previously established homology to the corresponding human gene locations based on canine:human chromosomal synteny. (upenn.edu)
  • Using the IMpRH 7000rad and IMNpRH2 12000rad radiation hybrid panels, these 5 genes mapped between microsatellite markers SWR67 and SW2067 . (biomedcentral.com)
  • We have characterized a panel of somatic cell hybrid cell lines which contain different portions of human chromosome 10. (ncsu.edu)
  • Genomic DNA from the somatic cell hybrids was tested for hybridization with each of an ordered set of probes used previously to construct a genetic map of chromosome 10, as well as several additional probes, previously localized by in situ hybridization. (ncsu.edu)
  • The resulting independently determined RH-map locations were compared with the corresponding gene locations from the draft sequence of the canine genome. (upenn.edu)
  • Moreover, once framework RH maps of a genome have been constructed, a quick location of markers by simple PCR on the RH panel is possible. (biomedcentral.com)
  • Finally, this RH map was used for testing the accuracy of the chicken genome assembly for chromosome 5. (biomedcentral.com)
  • The high resolution framework map obtained in this study has markers covering the entire chicken chromosome 5 and reveals the existence of a high number of rearrangements when compared to the human genome. (biomedcentral.com)
  • While in the process of finishing our map, the first draft sequence assembly of the chicken genome was released (March 1st, 2004). (biomedcentral.com)
  • VCMap can be used for many tasks such as: comparing QTL across species, viewing evolutionary rearrangements across species, comparing genome builds within species, comparing different map types within species, and so on. (animalgenome.org)
  • The recent draft assembly of the human genome provides a unified basis for describing genomic structure and function. (biomedcentral.com)
  • We describe numerous global features of the genome and examine the relationship of various genetic maps with the assembly. (biomedcentral.com)
  • The current coverage is, however, sufficient for the Human Genome Project to enter a new phase, in which the entire sequence can be analyzed to identify genes, regulatory regions and other genomic elements and structures. (biomedcentral.com)
  • However, the challenges in genome annotation remain daunting [ 10 ], and the research community can anticipate years of additional work and manual curation to produce a true gene map of high quality. (biomedcentral.com)
  • Here, we address these questions in the Alpine whitefish radiation, using a whole-genome dataset that includes multiple individuals of each of the 22 species belonging to six ecologically distinct ecomorph classes across several lake-systems. (biorxiv.org)
  • These results highlight the role of both genome architecture and secondary contact with hybridization in fuelling adaptive radiation. (biorxiv.org)
  • Using such approaches, studies have already highlighted the prevalence of either strongly differentiated genomic 'islands' of differentiation 5 - 10 or genome-wide polygenic architectures of phenotypic differentiation and ecological speciation 11 - 15 . (biorxiv.org)
  • Using the latest version of the draft sequence, the differentially expressed genes were mapped to the pig genome. (biomedcentral.com)
  • The dashed arrows outline an alternative strategy where comparisons are made on the human genome, using comparative mapping approaches. (biomedcentral.com)
  • Our findings provide insights into the alteration of potato genomes during the evolution of tuberization, and will enable genome design for new diploid hybrids. (nature.com)
  • A pan- Zea genome map for enhancing maize improvement. (zeagenomics.org)
  • Toward a physical map of the genome of the nematode Caenorhabditis elegans. (academicinfluence.com)
  • A backbone map is the primary map that will serve as the anchor off of which all comparative maps loaded will locate their sequence. (animalgenome.org)
  • To confirm the validity of the map and to provide valuable comparative mapping information, both markers from the genetic map and a high number of ESTs (Expressed Sequence Tags) were used. (biomedcentral.com)
  • This information was used to develop markers from chicken EST sequence data orthologous to genes in these human regions, in addition to the existing markers from the chicken chromosome 5 genetic map. (biomedcentral.com)
  • The quality of both the GGA5 RH map and of the sequence assembly was therefore checked by alignment of all the markers by BLAST searches. (biomedcentral.com)
  • Comparison of sequence data with the porcine BAC fingerprint map show that the cluster of genes resides in a 300 kb region. (biomedcentral.com)
  • genomic (sequence based), genetic (linkage based) and radiation hybrid (RH) . (animalgenome.org)
  • These sequence-based comparisons from UCSC define the anchors to allow cross-species comparisons across physical maps. (animalgenome.org)
  • Similarly, formerly independent maps, based on cytogenetic banding patterns, meiotic crossovers and radiation hybrids, may be placed within the single consensus sequence. (biomedcentral.com)
  • Public attention surrounding completion of the draft human sequence has fostered the impression that we are entering a 'post-genomic' era, and that description of genes and their functions is straightforward. (biomedcentral.com)
  • The resolution of radiation hybrid (RH) maps is intermediate between that of the genetic and BAC (Bacterial Artificial Chromosome) contig maps. (biomedcentral.com)
  • An important breakthrough in horse Y chromosome research came with the availability of new genomics tools and resources, such as large-insert genomic bacterial artificial chromosome (BAC) libraries (for review, see Rubes et al. (veteriankey.com)
  • All comparitive maps are based on the UCSC synteny for genomic maps. (animalgenome.org)
  • The available human/chicken comparative mapping data indicated conservation of synteny between GGA5 and portions of HSA11, HSA14 and HSA15. (biomedcentral.com)
  • Purpose: To facilitate the molecular characterization of naturally occurring cataracts in dogs by providing the radiation hybrid location of 21 cataract-associated genes along with their closely associated polymorphic markers. (upenn.edu)
  • Methods: Twenty-one genes with known mutations causing hereditary cataracts in man and/or mouse were selected and mapped to canine chromosomes using a canine:hamster radiation hybrid RH5000 panel. (upenn.edu)
  • Results: Twenty-one cataract orthologs were mapped to canine chromosomes. (upenn.edu)
  • When other comparative maps are loaded on top of that backbone, they will load all chromosomes that have syntenic regions that fall on the single chromosome of the backbone map, usually from more than one chromosome. (animalgenome.org)
  • When you load multiple maps from different species, all of the off-backbone maps are anchored relative to the single chromosome from the backbone map, often resulting in multiple chromosomes appearing for each off-backbone species. (animalgenome.org)
  • However, these maps will now be anchored to a new, different backbone and therefore, different homologous regions from different chromosomes may be loaded as well. (animalgenome.org)
  • A comparative radiation hybrid map of bovine chromosome 18 and homologous chromosomes in human and mice. (fbn-dummerstorf.de)
  • Comparative mapping of five coding DNA sequences on cattle chromosomes 7 and 25. (fbn-dummerstorf.de)
  • Studying the identity and genomic distribution of loci involved in ecological speciation, particularly in cases where parallel ecomorphological contrasts have arisen multiple times, is one way to address these questions. (biorxiv.org)
  • Each cataract gene ortholog was mapped in relation to over 3,000 markers including microsatellites, ESTs, genes, and BAC clones. (upenn.edu)
  • The final map is composed of 73 framework markers extending over a 1315.6 cR distance. (biomedcentral.com)
  • Linkage and physical maps are connected based on positions of markers sequences (STS) as recorded at UniSTS at NCBI. (animalgenome.org)
  • The RH maps are mapped to genomic assemblies based on the alignment of STS markers on both maps. (animalgenome.org)
  • Linkage and RH maps are only linked to other maps if they contain STS markers that also exist on those maps. (animalgenome.org)
  • VCMap was designed to fill a gap in the need for genomics viewers to compare QTL and annotations across species at a chromosomal level with multiple map types. (animalgenome.org)
  • Constraints on the design of primers were to avoid presence of long introns, whose position and length was predicted on the basis of the orthologous human gene structure, and to design primers in the most divergent regions of the human/chicken alignment, to limit cross-amplification with the hamster DNA present in the hybrids. (biomedcentral.com)
  • The panel of hybrid cell lines is thus useful for rapidly localizing unmapped probes and as a source of DNA for the construction of recombinant libraries derived from specific regions of the chromosome. (ncsu.edu)
  • We introduce MicroSyn software as a means of detecting microsynteny in adjacent genomic regions surrounding genes in gene families. (biomedcentral.com)
  • Screening the porcine CHORI-242 BAC library with a full-length AKR1C4 cDNA identified 7 positive clones and sample sequencing of 5 BAC clones revealed 5 distinct AKR1C genes ( AKR1CL2 and AKR1C1 through 4 ), which mapped to 126-128 cM on SSC10. (biomedcentral.com)
  • The probes have been used for molecular hybridizations (fluorescence in situ hybridization, or FISH) in clinical cytogenetics, Y chromosome mapping, sequencing, gene discovery, and comparative Y chromosome studies between the horse and other equids/ Perssodactyls. (veteriankey.com)
  • Targeted sequencing has emerged as a strong tool for estimating species trees in the face of rapid radiations, lineage sorting, and introgression. (frontiersin.org)
  • Moreover, our study contributes to the growing consensus that targeted sequencing data are a powerful tool in resolving rapid radiations. (frontiersin.org)
  • The loadable maps within VCMap have been gathered from multiple locations and have all been compiled by NCBI. (animalgenome.org)
  • VCMap was built to facilitate genomic visualization that enables discovery of genetic elements responsible for quantitative trait variation. (animalgenome.org)
  • Exploratory visualization of array-based comparative genomic hybridization. (auth.gr)
  • Hybridization of an unmapped probe to the cell line DNAs can be used to determine its most likely position on the chromosome relative to the mapped set of probes. (ncsu.edu)
  • Genomic DNA from two of the cell lines has been used to construct region-specific cosmid and bacteriophage libraries, and clones derived from these libraries were localized by hybridization to the panel of hybrid cell lines. (ncsu.edu)
  • Characterization of radiation/fusion hybrids containing parts of human chromosome 10 and their use in mapping chromosome 10-specific probes. (ncsu.edu)
  • MicroSyn searches for conserved, flanking colinear homologous gene pairs between two genomic fragments to determine the relationship between two members in a gene family. (biomedcentral.com)
  • Conversely, substitution of chromosome 18 from SS to the BN strain (BN‐18 SS ) resulted in a relatively small increase in MAP in response to the high‐salt diet. (comprehensivephysiology.com)
  • We also identify 561,433 high-confidence structural variants and construct a map of large inversions, which provides insights for improving inbred lines and precluding potential linkage drag, as exemplified by a 5.8-Mb inversion that is associated with carotenoid content in tubers. (nature.com)
  • 2012). Virtual Comparative Map (VCMap): A comparative genomics tool designed to facilitate cross-species annotation. (animalgenome.org)
  • Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process. (zeagenomics.org)
  • In the current version of VCMap, if you wish to load genetic or radiation hybrid comparative map, the genomic version of that map must be loaded before the genetic or radiation hybrid comparative map. (animalgenome.org)
  • Radiation hybrid maps have a resolution power intermediate to that of the genetic and BAC contig maps and are also a powerful tool for the mapping of ESTs and genes by simple PCR. (biomedcentral.com)
  • Genomic insights into historical improvement of heterotic groups during modern hybrid maize breeding. (zeagenomics.org)
  • Despite the supposed prevalence of ecological speciation in adaptive radiation, the factors that constrain or facilitate speciation and the mechanisms by which speciation proceeds during the adaptive radiation of lineages are still not well understood 3 , 4 . (biorxiv.org)
  • This could be improved by further comparative mapping analyses but this would be time consuming. (biomedcentral.com)
  • Several of these probes reveal restriction fragment length polymorphisms which have been genetically mapped. (ncsu.edu)
  • The recent development of canine genomic resources make canine models a practical and valuable resource for the study of human hereditary cataracts. (upenn.edu)
  • Assignment of the human postmeiotic segregation increased (S. cerevisiae) 1 (PMS1) to chromosome 2q31.1 by radiation hybrid mapping. (nih.gov)
  • The chicken ChickRH6 panel recently produced was used here to construct a high resolution RH map of chicken GGA5. (biomedcentral.com)
  • The 'Swap Backbone' feature of VCMap allows you to view the currently loaded maps from the opposite angle. (animalgenome.org)
  • After clicking the 'Search' button, VCMap will begin searching the currently loaded maps and the data from its database. (animalgenome.org)
  • Understanding the genetic basis of speciation and adaptive radiation without geographic isolation, and determining how and when such diversification is possible, is a key aim of evolutionary biology. (biorxiv.org)
  • Because of the large size of the datasets related to genomic data, it is often difficult to visualize all data at once. (animalgenome.org)
  • With large overlapping pieces of annotation, for example QTL, the annotation may be placed into groups if more than three features overlap in the same area of the map. (animalgenome.org)
  • QTL mapping and mining for functional candidate genes affecting health - the German ADR QTL Dairy Cattle Project. (fbn-dummerstorf.de)
  • For the backbone map, you must specify a single chromosome to be loaded at a time. (animalgenome.org)
  • That is, when you swap backbones, you can choose a single chromosome from an off-backbone map to become the new backbone. (animalgenome.org)