User:Ilya/BioBrick aligner

Description

BioBricks 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

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. DOI:10.1101/gr.8.9.967 |