User:Ilya/BioBrick aligner: Difference between revisions

Revision as of 15:40, 23 July 2007

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

based on Sim4 - a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene
A computer program for aligning a cDNA sequence with a genomic DNA sequence (backup link)
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)

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 [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 Sim4] is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene
+*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
 *[[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])
 *[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