MoMo: Discovery of post-translational modification motifs

Abstract

MotivationPost-translational modifications (PTMs) of proteins are associated with many significant biological functions and can be identified in high throughput using tandem mass spectrometry. Many PTMs are associated with short sequence patterns called \"motifs\" that help localize the modifying enzyme. Accordingly, many algorithms have been designed to identify these motifs from mass spectrometry data.\n\nResultsMoMo is a software tool for identifying motifs among sets of PTMs. The program re-implements two previously described algorithms, Motif-X and MoDL, packaging them in a web-accessible user interface. In addition to reading sequence files in FASTA format, MoMo is capable of directly parsing output files produced by commonly used mass spectrometry search engines. The resulting motifs are presented to the user in an HTML summary with motif logos and linked text files in MEME motif format.\n\nAvailabilitySource code and web server available at http://meme-suite.org\n\nContacttimothybailey@unr.edu and william-noble@uw.edu\n\nSupplementary informationSupplementary figures are available at Bioinformatics online.