1Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund 44227, Germany2Proteomics Unit, Department of Biomedicine3Computational Biology Unit, Department of Informatics4KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway5Department of Pediatrics, Haukeland University Hospital, Bergen, Norway6College of Physical Sciences, University of Aberdeen, Old Aberdeen AB24 3UE, UK7Medizinische Fakultät, Ruhr-Universität Bochum, Bochum 44801, Germany8Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
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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.Contact:firstname.lastname@example.org or email@example.comSupplementary information:Supplementary data are available at Bioinformatics online.