Sequence Analysis:

Activities pursued in this area have a direct bearing on genomics projects with the bioinformatics unit providing sequence analysis services on these projects. Research activities include a dapting and developing nucleotide sequence analysis algorithms for orthology detection, marker prediction, extraction of information from model crop genomes and interpretation of evolutionary scenarios. Two molecular marker databases have been published online, both constructed from public sequence data and relevant to ICRISAT mandate crops: an SSR (simple sequence repeats) database (http://www.intranet.icrisat.org/gt1/SSR/SSRdatabase.html) and a database of tentative orthologous groups specifically derived from stress transcripts (http://www.intranet.icrisat.org/gt1/tog/homepage.htm). Marker detection algorithms have been implemented as software tools, such as the CISprimer Tool . Several parsing and formatting scripts are made available to laboratory staff; these include Blast output parsing tools (Blast output analyzer), Perl and Java scripts for formatting sequence data, functional annotation of EST data (http://www.icrisat.org/gt-bt/cpest/home.asp), identification of tandem repeats, development of degenerate primer pairs and in silico PCR.