User:Ilya/BioBrick aligner

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Current revision (13:54, 1 June 2011) (view source)
 
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[http://habanero.mit.edu/cgi-bin/biobricks.pl BioBricks aligner] - aligns sequence reads (fragments) to Biobrick sequence
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==Description==
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*based on [http://bioinformatics.ubc.ca/resources/tools/index.php?name=sim4 Sim4] - a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene
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[http://habanero.mit.edu/cgi-bin/biobricks.pl BioBrick aligner] - aligns sequence reads (fragments) to Biobrick sequence
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*[[doi:10.1101/gr.8.9.967|A computer program for aligning a cDNA sequence with a genomic DNA sequence]] ([http://www.genome.org/cgi/content/full/8/9/967 backup link])
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==Requirements==
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*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)
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*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
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==References==
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<biblio>
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Miller-1998 pmid=9750195
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</biblio>

Current revision

Description

BioBrick aligner - aligns sequence reads (fragments) to Biobrick sequence

Requirements

References

  1. Florea L, Hartzell G, Zhang Z, Rubin GM, and Miller W. . pmid:9750195. PubMed HubMed [Miller-1998]
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