COGEM: A Toolbox for Computational Genomics in Matlab

Abstract

MotivationThe Matlab programming language is widely used for both teaching and research in engineering, computer science, and mathematics. Despite its many strengths, it has never been a dominant language in computational genomics or bioinformatics more generally.\n\nResultsHere, we introduce COGEM, a long-term project to develop computational genomics functionality in Matlab. The initial release provides functions for manipulating genomic intervals, stranded or unstranded, with or without numerical data associated. It includes features for both text and binary file input and output, conversion between BAM, BED and BEDGRAPH formats, and numerous functions for manipulating intervals, including shifting, expanding, overlapping, intersecting, unioning, finding nearest intervals, piling up intervals, and performing unary and binary numerical and logical operations on sets of intervals. The toolbox is well-suited to the analysis of high-throughput sequencing data. We demonstrate its functionality by creating a ChIP-seq peak-calling algorithm by chaining together a series of commands, and find it capable of analyzing genome-scale data in reasonable time.\n\nAvailabilityThe current toolbox and reference manual is available as supplementary material, and updated versions will be maintained at www.perkinslab.ca online.