PeptideMapper: Efficient and versatile amino acid sequence and tag mapping

Abstract

The mapping of amino acid sequences is an essential task in bioinformatics. Notably, the mapping of peptide sequences on a proteome is required for the post-processing of proteomics results. However, this step can quickly become a bottleneck when working with extensive numbers of peptides or large protein sequence databases. Here, we present PeptideMapper, a novel amino acid sequence mapper for both peptide sequences and de novo sequencing identification results. By taking advantage of the latest advances in pattern matching, PeptideMapper achieves unprecedented performance (i.e. up to 1000 faster than state-of-the-art software) in terms of memory footprint and execution speed, with regards to both the indexing and the querying of protein sequence databases. Availability and Implementation: PeptideMapper is implemented in the open source Java CompOmics framework under the permissive Apache 2.0 license https://github.com/compomics/compomics-utilities.