title: pfsearchV3: a code acceleration and heuristic to search PROSITE profiles.
abstract: CONCLUSIONS
  The PROSITE resource provides a rich and well annotated source of signatures in the form of generalized profiles that allow protein domain detection and functional annotation. One of the major limiting factors in the application of PROSITE in genome and metagenome annotation pipelines is the time required to search protein sequence databases for putative matches. We describe an improved and optimized implementation of the PROSITE search tool pfsearch that, combined with a newly developed heuristic, addresses this limitation. On a modern x86_64 hyper-threaded quad-core desktop computer, the new pfsearchV3 is two orders of magnitude faster than the original algorithm.
  
  
  METHODS
  Source code and binaries of pfsearchV3 are freely available for download at http://web.expasy.org/pftools/#pfsearchV3, implemented in C and supported on Linux. PROSITE generalized profiles including the heuristic cut-off scores are available at the same address.
authors.affiliation: Vital-IT Group, SIB Swiss Institute of Bioinformatics, Genopode, UNIL-Sorge, 1015 Lausanne, Switzerland.
authors.forename: Thierry
authors.initials: T
authors.lastname: Schuepbach
authors.forename: Marco
authors.initials: M
authors.lastname: Pagni
authors.forename: Alan
authors.initials: A
authors.lastname: Bridge
authors.forename: Lydie
authors.initials: L
authors.lastname: Bougueleret
authors.forename: Ioannis
authors.initials: I
authors.lastname: Xenarios
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Cerutti
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D058977:Molecular Sequence Annotation; D017434:Protein Structure, Tertiary; D020539:Sequence Analysis, Protein; D012984:Software