Plant, Animal & Microbe Genomes X Conference Plant, Animal & Microbe Genomes X ConferenceJanuary 12-16, 2002
Town & Country Convention Center
San Diego, CA
Bioinformatics: Databases
We have developed a porcine expressed sequence tagged (EST) database, a set of tools for EST analysis and a web query tool for public access to this database. A collection of 14,602 public ESTs from 20 cDNA libraries (whole embryo, fetus, term placenta, anterior pituitary, hypothalamus, ovary and uterus) were utilized. Nucleotide similarities between pig ESTs and human genes were determined by BLAST against 92,152 human UniGene sequences. LocusLink , UniSTS and radiation hybrid (RH) map location were used to order the putative human orthologs of pig ESTs on human chromosomes. The pig-on-human comparative maps and homology between pig and human chromosomes were then used to predict pig EST assignments on pig chromosomes. The similarities among Pig ESTs and 3,331 pig genes retrieved from GenBank were also examined. A number of PERL scripts were written for parsing the BLAST output and integrating related information. Results showed that the pig ESTs hits 2,156 human UniGenes with cytogenetic information and 1,427 pig ESTs had a significant hit (score >200) to 508 pig gene sequences.. A pig EST database has been created. Database administration and web query tools were developed using the DBI PERL module. This database is comprised of a number of tables covering the EST profile, alignment similarity, human ortholog information on cytogenetic, linkage, and RH locations. Interactive web query interfaces are developed for public access to the EST database (http://pigest.genome.iastate.edu). Based on the current work, public EST data will be added to generate a more diverse pig EST database.