The Grassius Regulatory Grid eXplorer
is a web application for visually accessing regulatory networks.
"The Basic Local Alignment Search Tool (BLAST
) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families." (Taken from NCBI)
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool.
J Mol Biol. 1990 Oct 5;215(3):403-10.
Perl scripts or modules used in GRASSIUS
Perl Modules (all available at CPAN or bioperl.org)
- HTML::Mason module is used to embed Perl in HTML and generate webpages
- BioPerl modules are used to handle, modify and parse sequence data. Latest version of Bioperl can be obtained from bioperl.org
- Bio::Graphics module, part of BioPerl module, is used to generate visual representations of protein domains, gene structures, cis-regulatory elements, etc.
Custom Perl scripts
- Script to identify redundant sequences within a multi-fasta file (uses Digest::MD5 module). Download
- Script to sort proteins into TF families based on PFAM output. Download