Go to the abstract in the NAR 2003 Database Issue.
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http://bioinfo.weizmann.ac.il/udb/
Chalifa-Caspi, V, Safran, M., Lapidot, M., Rosen, N., Lancet, D.
The Weizmann Institute of Science Rehovot, Israel
Contact marilyn.safran@weizmann.ac.il
UDB presents an integrated map for each human chromosome, based on data from various radiation hybrid, linkage and physical mapping resources, and further improved by anchorage of NCBI's genomic contigs (containing finished and unfinished sequences), and repositioning of markers, genes and EST clusters in the sequenced regions. Due to its tabular output format and extensive set of genomic markers, UDB is especially useful for obtaining a bird’s-eye view of genomic regions in linkage analysis and gene discovery projects. Originally, the UDB map was based on Sequence Tagged Sites (STSs), genetic and radiation hybrid markers from different resources, combined using an interpolation algorithm into a single megabase scale map for each chromosome. Subsequently, EST clusters were anchored to the map according to their included markers. For clusters identified as known genes, the symbols were also included and linked to GeneCards. Later versions applied a Sequence-Based Repositioning (SBR) algorithm, which incorporated genomic contig sequence data into the map, using it to generate more accurate relative positions. A crucial step in building UDB was the establishment of a thesaurus for primary names and aliases of genomic markers. Marker names often differ among the sources; UDB combines them under a unique identifier. This thesaurus currently contains 154,120 markers. Further, UDB stores the primer sequences and product sizes of the STSs. Using the electronic PCR program more than 100,000 STSs were placed on the sequence-based UDB map. About 8,413 STSs were found to be associated with more than one location in the genomic sequences; these non-unique markers were rejected, unless they appeared only twice, with the two less than 1 Mb apart. A Web-based form enables one to specify the region of interest as a cytogenetic band, a genomic interval or as genomic objects such as markers, genes or EST clusters. Both primary names and aliases may be entered as keywords. The selected map region is displayed in a customizable tabular format. Each row represents a location on the integrated map, with indicated UDB megabase coordinates. Each column shows objects of a different class - markers, genes or clusters. For markers, additional details appear, including DS-number, polymorphic nature, cDNA origin and specific map affiliation. For every marker, an internal link is provided to a MarkerCard which lists additional details retrieved from the sources, including original map data, full DNA sequence and flanking primers, synonymous names and heterozygote frequency for linkage markers.
Category Genetic and Physical Maps
Go to the abstract in the NAR 2003 Database Issue.