User:Ilya/BioBrick aligner: Difference between revisions
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(New page: [http://habanero.mit.edu/cgi-bin/biobricks.pl BioBricks aligner] - aligns sequence reads (fragments) to Biobrick sequence *[http://bioinformatics.ubc.ca/resources/tools/index.php?name=sim4...) |
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[http://habanero.mit.edu/cgi-bin/biobricks.pl | ==Description== | ||
*[http:// | [http://habanero.mit.edu/cgi-bin/biobricks.pl BioBrick aligner] - aligns sequence reads (fragments) to Biobrick sequence | ||
==Requirements== | |||
*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 | ||
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*[http://search.cpan.org/~birney/bioperl-1.4/Bio/Tools/Sim4/Results.pm Bio::Tools::Sim4::Results] - results of one Sim4 run | *[http://search.cpan.org/~birney/bioperl-1.4/Bio/Tools/Sim4/Results.pm Bio::Tools::Sim4::Results] - results of one Sim4 run | ||
*[http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-run/Bio/Tools/Run/Alignment/Sim4.pm Sim4.pm] - CVS log (latest version) | *[http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-run/Bio/Tools/Run/Alignment/Sim4.pm Sim4.pm] - CVS log (latest version) | ||
*also requires a version of [http://search.cpan.org/~sendu/bioperl/Bio/Graphics/Panel.pm Bio::Graphics::Panel] module ([http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Graphics/Panel.html CPAN documentation]) that has image_and_map() function | |||
==References== | |||
<biblio> | |||
Miller-1998 pmid=9750195 | |||
</biblio> | |||
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
