 |
 |
|||||||||||
|
||||||||||||
|
||||||||||||
Research
Applied Genomics |
Global research themes GT-Harnessing biotechnology Bioinformatics Sequence Analysis |
|---|
Bioinformatics Sequence analysis
Sequence Analysis
Sequence analysis scripts, pipelines, and other software The Bioinformatics Unit develops and hosts pipelines and software analysis tools for sequence analysis which are of direct interest to genomics projects being carried out at the CEG. Research activities include adapting and developing nucleotide sequence analysis algorithms for orthology detection, marker prediction, extraction of information from model crop genomes and interpretation of evolutionary scenarios. Current interest is also focused on Next Generation Sequence analysis software. 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/what-we-do/biotechnology/Cpest/home.asp), identification of tandem repeats, development of degenerate primer pairs and in silico PCR, SNP detection and diversity statistics prediction modules.
Licensed sequence analysis software available at the Bioinformatics unit include Sequencher 4.0.2 (Gene Codes Corporation) and PAUP 4.0 (Sinauer Associates). Public domain software hosted include PHYLIP3.6, CLUSTALW1.8, CAP3, PCAP, Gblocks, PAML
(http://abacus.gene.ucl.ac.uk/software/paml.html), CMTV
(http://sourceforge.net/projects/cmtv), CODEHOP, DNAsp, K-Estimator, MISA, the PISE software environment. Several NGS data analysis software are currently being benchmarked and will be made available soon on the HPC with parsing/glue scripts.
