Plant & Animal Genomes XV Conference Plant & Animal Genomes XV ConferenceJanuary 13-17, 2007
Town & Country Convention Center
San Diego, CA
Timothy J Close , Steve I Wanamaker , Matthew Lyon , Mikeal L Roose
HarvEST is viewing software for sequence assemblies composed mainly of ESTs. The software, now available for barley, Brachypodium, citrus, coffee, rice, soybean and wheat, can be operated online at http://138.23.191.142/hweb/ and is freely distributed for local Windows installation from http://harvest.ucr.edu. EST sequences typically have been quality trimmed, cleaned of vector, and assembled using CAP3 and quality values. For most functions, no Internet connection is required such that the portable software is fully operational. Each version contains a choice of assemblies. Displays include sequence alignment, library sources, locations of orthologs on rice and Arabidopsis genetic maps. The software provides archived BLAST hit and UniProt information, unigene export, Boolean searching with user-defined quantitative settings, and several other searching, reporting and export functions. The unigene export feature can be applied to an entire assembly, a single or multiple libraries, or from the output of any other search. Searches can be initiated using keywords, gene frequency in designated source libraries, GenBank accession numbers, or lists of probe sets represented on Affymetrix chips. Content for the Affymetrix barley and citrus microarrays was based on the HarvEST assemblies, which makes it possible to display exact locations of probes in the alignment views. Output can be viewed on-screen or exported as summary tables or sequence files. HarvEST contains links to NCBI, TIGR and UniProt databases. HarvEST development has been supported by funding from the USDA Plant Genome Program, National Science Foundation Plant Genome Research Program, California Citrus Research Board and the UC Discovery Grants Program.