User:Ilya/BioBrick aligner

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==Description==
==Description==
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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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[http://habanero.mit.edu/cgi-bin/biobricks.pl BioBrick aligner] - aligns sequence reads (fragments) to Biobrick sequence
==Requirements==
==Requirements==
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*based on [http://bioinformatics.ubc.ca/resources/tools/sim4 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>
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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

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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