User:Ilya/BioBrick aligner

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[edit] Description

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

[edit] 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

[edit] References

1. Florea L, Hartzell G, Zhang Z, Rubin GM, and Miller W. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res 1998 Sep; 8(9) 967-74. pmid:9750195. PubMed HubMed [Miller-1998]