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This collection of tools forms the basis of a pipeline for the complete enumeration of the number of solutions present in a model that maximizes a single objective function.

ExonFinder provides a pipeline to extract novel cassette exons and novel retained-introns from the results of mapping cross-species ESTs against a target genome via blat.

To get access to the code, please check it out with svn as described in the code section.

This is an approach that complements previous methods for reliable homozygous structural variation identification. Our approach accurately determines genotype and breakpoints relative to a reference genome based on de novo assembly of Illumina Genome Analyzer sequencing data. In this method, we examined only homozygous structural variations because detecting heterozygous structural variations requires assembly of haplotype sequences, which is not yet possible using existing assemblers.

SIPeS - Site Identification from Paired-end Sequencing

An SQL handler to interface multiple databases data to the OpeNDAP Hyrax (BES) server. Written in C++, it uses unixODBC to query DB and can be dynamically extended to use proprietary ODBC API driver in many easy ways. It is bundled with scripts to ge