UProC: tools for ultra-fast protein domain classification.

Abstract

With rapidly increasing volumes of biological sequence data the functional analysis of new sequences in terms of similarities to known protein families challenges classical bioinformatics. The ultrafast protein classification (UProC) toolbox implements a novel algorithm ('Mosaic Matching') for large-scale sequence analysis. UProC is by three orders of magnitude faster than profile-based methods and in a metagenome simulation study achieved up to 80% higher sensitivity on unassembled 100 bp reads. UProC is available as an open-source software at https://github.com/gobics/uproc. Precompiled databases (Pfam) are linked on the UProC homepage: http://uproc.gobics.de/. peter@gobics.de. Supplementary data are available at Bioinformatics online.