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pftools: a suite of tools to build and search generalized profiles

The pftools package contains all the software necessary to build protein and DNA generalized profiles and use them to scan and align sequences, and search databases.

Documentation | Downloads | pfsearchV3 | References


Documentation describing the pftools file formats and the individual software components:



The new pfsearchV3 program replaces the original pfsearch program distributed with the pftools. It uses modern CPU instructions to exploit the capabilities of multicore processors and a new heuristic filter to rapidly score and select possible candidate matches. On a modern dual-threaded 8 cores computer these improvements increase the speed of pfsearch by 2 orders of magnitude.


  1. Lüthy R, Xenarios I, Bucher P (1994) Improving the sensitivity of the sequence profile method. Protein Sci 3:139-46. (PubMed)
  2. Bucher P, Karplus K, Moeri N, Hofmann K (1996) A flexible motif search technique based on generalized profiles Computers chemistry 20: 3-23. (PubMed)
  3. Sigrist CJ, Cerutti L, Hulo N, Gattiker A, Falquet L, Pagni M, Bairoch A, Bucher P (2002) PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform 3: 265-74. (PubMed)