Plant & Animal Genomes XI Conference Plant & Animal Genomes XI ConferenceJanuary 11-15, 2003
Town & Country Convention Center
San Diego, CA
Bioinformatics: Software
Computer: Poster and Demo
HarvEST is EST database-viewing software that emphasizes gene function and is oriented to comparative genomics and the design of oligonucleotides, in support of activities such as microarray content design, physical mapping, and genetic mapping. HarvEST: Triticeae contains more than 400,000 EST’s from wheat and barley projects worldwide, and may be downloaded from http://harvest.ucr.edu. Most functions of HarvEST require no Internet connection. This includes: unigene export from archived contig assemblies, Boolean searching with user-defined quantitative settings, archived BLAST hit information, and various other searching, reporting and export functions. Unigene export can be applied to entire assemblies, individual libraries, or combinations of libraries. For Boolean searches, a user sets search parameters according to their interest. For example, the choice could be genes associated with a particular stress (e.g. low temperature, heat, drought, aluminum, nitrogen deprivation), developmental stage (e.g. malted seed, pre-anthesis spike), or tissue (e.g. endosperm, pericarp, embryo sac, rachis, root tip). The user also decides what percentage representation is relevant. The search is fully executed quickly, and a browsable output is displayed. The output can be viewed on-screen or exported as summary tables or sequence files. HarvEST also facilitates connection to NCBI for live BLAST searches of dbEST. All EST sequences in HarvEST have been quality trimmed, cleaned of vector, and CAP3-assembled. Subsequent versions will respond to user feedback, and contain updated information and new functions, including web-operability. We are happy to discuss partnerships to apply the HarvEST shell to EST sequence data from any organism.