Package: sigma-align (1.0-1)

Simple greedy multiple alignment of non-coding DNA sequences

Sigma ("Simple greedy multiple alignment") is an alignment program with a new algorithm and scoring scheme designed specifically for non-coding DNA sequence. It uses a strategy of seeking the best possible gapless local alignments, at each step making the best possible alignment consistent with existing alignments, and scores the significance of the alignment based on the lengths of the aligned fragments and a background model which may be supplied or estimated from an auxiliary file of intergenic DNA. With real data, while "correctness" can't be directly quantified for the alignment, running the PhyloGibbs motif finder on pre-aligned sequence suggests that Sigma's alignments are superior. It has been published in BMC Bioinformatics. 2006 Mar 16;7:143.

Homepage: http://www.imsc.res.in/~rsidd/sigma/

Tags: Field: Biology, Implemented in: OCaml, User Interface: Command Line, Role: Program, Scope: Utility, Supports Format: Plain Text