User:Ilya/BioBrick aligner: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
m (→Description) |
No edit summary |
||
Line 3: | Line 3: | ||
==Requirements== | ==Requirements== | ||
*based on [http:// | *based on [http://sibsim4.sourceforge.net/ Sim4] - a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene <cite>Miller-1998</cite> | ||
*[http://search.cpan.org/~birney/bioperl-run-1.4/Bio/Tools/Run/Alignment/Sim4.pm Bio::Tools::Run::Alignment::Sim4] - wrapper for Sim4 program that allows for alignment of cdna to genomic sequences | *[http://search.cpan.org/~birney/bioperl-run-1.4/Bio/Tools/Run/Alignment/Sim4.pm Bio::Tools::Run::Alignment::Sim4] - wrapper for Sim4 program that allows for alignment of cdna to genomic sequences | ||
*[http://search.cpan.org/~birney/bioperl-1.4/Bio/SearchIO/sim4.pm Bio::SearchIO::sim4] - parser for Sim4 alignments | *[http://search.cpan.org/~birney/bioperl-1.4/Bio/SearchIO/sim4.pm Bio::SearchIO::sim4] - parser for Sim4 alignments |
Latest revision as of 11:54, 1 June 2011
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