Plant & Animal Genomes XI Conference Plant & Animal Genomes XI ConferenceJanuary 11-15, 2003
Town & Country Convention Center
San Diego, CA
Bioinformatics: Databases
Computer: Poster and Demo
A marker anchored physical map of the soybean genome derived from large insert clones has been constructed. Here we describe the three sets of tools available to access the datasets. One route of access is provided by genetic markers. The map is anchored by microsatellite and RFLP markers. There is a search tool for individual markers at www.siu.edu/~pbgc/htmls/search.html. The genetic map location of a marker on the USDA linkage group can be viewed at www.siu.edu/~pbgc/htmls/link.htm. Selecting http://www.siu.edu/~pbgc/htmls/mapa1.htm allows the genetic map of a particular linkage group to be displayed. Selecting a marker within that group allows the contig(s) identified by that marker to be displayed with clone plate addresses. Selecting a the (NCBI) button next to a marker allows the DNA sequences associated with that marker to be displayed. These include primer sequences, allele sequences, BAC end sequences and sequence tagged sites linked to clone plate addresses within that contig. The sequences associated with a contig represent a second route of entry to the physical map. A third route of access is provided by the plate addresses for clones that can be used to view individual BAC fingerprints at http://hbz.tamu.edu/- Physical Mapping/Soy Map. At this site fingerprints were used to create an FPC database for investigator driven contig assembly http://hbz.tamu.edu/bacindex1.html. Contigs representing the soybean physical map have been assembled and posted at this site. Three of five envisioned search tools are available, BAC clone plate address to FPC fingerprint; BAC clone plate address to contig; and contig number to contig map. All contigs show plate addresses that identify libraries correctly. A downloadable FPC database will be made available so that individuals can generate their own builds and merges using fingerprint data. The whole database structure will be mirrored at two sites to avoid loss of access. The databases are being incorporated into a GMOD genome browser format with an FPC plug in that allows DAS applications. These resources are made available so that community members can use the database to build their own overlapping clone tiles, to provide a framework for EST mapping, to allow comparative genome analysis between cultivars, to support large-scale genome sequencing and to direct targeted DNA marker development. This work was supported by NSF project #9872635.