Cargando…

UProC: tools for ultra-fast protein domain classification

Motivation: 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. Results: The ultrafast protein classification (UProC) toolbox implements a novel algorithm (‘Mosaic...

Descripción completa

Detalles Bibliográficos
Autor principal: Meinicke, Peter
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410661/
https://www.ncbi.nlm.nih.gov/pubmed/25540185
http://dx.doi.org/10.1093/bioinformatics/btu843
Descripción
Sumario:Motivation: 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. Results: 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. Availability and implementation: 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/. Contact: peter@gobics.de. Supplementary information: Supplementary data are available at Bioinformatics online.