Multiple Alignment Format parser for BioRuby

by Clayton Wheeler for Open Bioinformatics Foundation

The MAF (Multiple Alignment Format) file format has become popular in bioinformatics for representing similarities, in the form of sequence alignments, between multiple whole genomes. Such multiple sequence alignments enable many kinds of analysis, including examination of the phylogenetic relationships between organisms, of conserved regions of DNA potentially indicating functionally important sequences, and making inferences about genomes by reference to more fully annotated genomes (Blankenberg et al., 2011). Although BioRuby supports multiple sequence alignments through the bio-alignment gem, it does not currently support the MAF format. This project aims to rectify that by creating a bio-alignment plugin to provide full MAF support from a native BioRuby interface. This is particularly important as MAF files can often be in the hundreds of gigabytes and are often queried and filtered in a rich way; programmatic access to them is valuable for the same reasons programmatic access to databases is indispensable. Having native BioRuby support for MAF will thus allow use of the sizable BioRuby toolset with this data, and also make BioRuby a more viable tool for an important class of problems.