Plant, Animal & Microbe Genomes X Conference Plant, Animal & Microbe Genomes X ConferenceJanuary 12-16, 2002
Town & Country Convention Center
San Diego, CA
Bioinformatics: Databases
There has been a dramatic increase in expressed sequence tags (ESTs) generated in recent years for the Triticeae tribe crops (especially Triticum aestivum and Hordeum vulgare). A database has been constructed to serve the EST information utilizing ACEDB and mySQL database resources. The information is also made available to the WWW using the AcePerl/AceBrowser package. These ESTs can be useful in determining potential candidate genes by linking to public database resources such as NCBI. Currently, over 80,000 wheat sequences have been entered into the wEST database from the local project site. These sequences have been processed to remove poor quality read and vector regions; however, original trace files for these sequences are available from a trace server linked to from GrainGenes. While GrainGenes provides a wide range of information on the small grains (e.g. genetic maps, gene sequences and classifications, phenotypes, including other classical trait information), the wEST database provides additional genomic information on the sequences which have been produced. About 7900 Contigs have been generated in preliminary consensus assemblies and links have been made to other assemblies constructed by TIGR and NCBI. Additional EST sequences from related projects have been added for comparison. Data from an NSF-sponsored project have been added to the database to display mapped positions of ESTs used as probes hybridized to an aneuploid series of wheat deletion lines (B. Gill et al.). Currently, over 1400 probes have generated more than 4800 tentatively mapped loci in bins of the 21 chromosomes for hexaploid cv. Chinese Spring wheat. Tools are being developed to better display the links between EST candidate loci and GrainGenes data. The wEST database is accessible from http://wheat.pw.usda.gov/wEST.