User:Ilya/BioBrick aligner: Difference between revisions
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==Description== | ==Description== | ||
[http://habanero.mit.edu/cgi-bin/biobricks.pl | [http://habanero.mit.edu/cgi-bin/biobricks.pl BioBrick aligner] - aligns sequence reads (fragments) to Biobrick sequence | ||
==Requirements== | ==Requirements== | ||
Revision as of 15:59, 23 July 2007
Description
BioBrick aligner - aligns sequence reads (fragments) to Biobrick sequence
Requirements
- based on Sim4 - a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene [1]
- Bio::Tools::Run::Alignment::Sim4 - wrapper for Sim4 program that allows for alignment of cdna to genomic sequences
- Bio::SearchIO::sim4 - parser for Sim4 alignments
- Bio::Tools::Sim4::Exon - a single exon determined by an alignment
- Bio::Tools::Sim4::Results - results of one Sim4 run
- Sim4.pm - CVS log (latest version)
- also requires a version of Bio::Graphics::Panel module (CPAN documentation) that has image_and_map() function
