Plant, Animal & Microbe Genomes X Conference Plant, Animal & Microbe Genomes X ConferenceJanuary 12-16, 2002
Town & Country Convention Center
San Diego, CA
Bioinformatics: Software
Computer: Poster and Demo
HarvEST is Windows software, developed initially for the Triticeae (wheat, barley, rye) that facilitates browsing of EST databases. One feature allows the user to search for EST's that are differentially expressed among cDNA libraries using a simple Boolean operation with user-controlled quantitative threshold settings. In this operation two types of sets are considered: 1) contigs, defined by EST sequence similarities and 2) library of origin of the EST sequences. For example the user can ask, What sequences exist at a frequency of at least 0.25% in any cold-acclimated library but less than 1/10 of that frequency in libraries made from equivalent non-acclimated tissues? The search output displays a list of EST contigs that fulfill the search parameters, the best BLAST hit, and a summary of the distribution of ESTs that comprise the contig in all libraries. Another feature of HarvEST is facilitated searches of NCBI databases, for example Find a Triticeae EST for Your Favorite Gene. Other features include a keyword search of best BLAST annotations and general EST lookup functions. The HarvEST Triticeae package contains ESTs from the NSF wheat (http://wheat.pw.usda.gov/NSF/) and USDA barley (http://www.genome.clemson.edu/projects/barley/) projects. As of October 12, 2001 approximately 114,000 Triticeae ESTs were included in version 0.62 of HarvEST Triticeae. The HarvEST Triticeae software can be downloaded as an ~40 MB compressed file from http://harvest.ucr.edu, where screen shots are shown. We encourage user feedback. Subsequent versions of HarvEST Triticeae will include additional Triticeae ESTs and incorporate additional contig assemblies. HarvEST can also be used to browse non-Triticeae contig assemblies. We welcome contig assemblies and advice that will allow HarvEST to be applied to other plants or non-plant organisms.