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.

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Documentation | Downloads | pfsearchV3 | References | Contact

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Documentation

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

• File formats used by the pftools
  • Generalized profiles format and syntax.
  • The multiple sequence alignment format (PSA).
  • The extended header multiple sequence alignment format (XPSA).
    
    
• Programs to build generalized profiles

  pfmake

  Build a profile from a multiple sequence alignment. (manual page)

  pfscale

  Fit parameters of an extreme-value distribution to a profile score list. (manual page)

  pfw

  Weight sequences of a multiple sequence alignment to correct for sampling bias. (manual page)

• Programs to search with generalized profiles

  pfsearch

  Search a protein or DNA sequence library for sequence segments matching a profile. (manual page)

  pfscan

  Scan a protein or DNA sequence with a profile library. (manual page)

• Conversion programs

  psa2msa

  Reformat PSA file to Pearson/Fasta multiple sequence alignment file. (manual page)

  ptof

  Convert a protein profile into a frame-search profile to search DNA sequences. To be used with 2ft. (manual page)

  2ft

  Converts both strands of DNA into so-called interleaved frame-translated DNA sequences to search with protein profiles. To be used with ptof. (manual page)

  6ft

  Translates all six reading frames of a double-stranded DNA sequence into individual protein sequences. (manual page)

  gtop

  Convert a profile in GCG format into PROSITE format. (manual page)

  htop

  Convert a HMMER1 ASCII-formatted HMM into an equivalent PROSITE profile. (manual page)

  ptoh

  Converts a generalized profile into an approximately equivalent HMM profile in HMMER1 format (can be read by the hmmconvert program from the HMMER2 package). (manual page)

• A short technical document about the algorithm used to build generalized profiles.

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Documentation | Downloads | pfsearchV3 | References | Contact

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Downloads

• The latest stable release of the pftools: ftp://lausanne.isb-sib.ch/pub/software/unix/pftools/pft2.3/latest.tar.gz.
• The current development release: ftp://lausanne.isb-sib.ch/pub/software/unix/pftools/pft2.3/dev.tar.gz.
• The pre-compiled binaries of the stable release: ftp://lausanne.isb-sib.ch/pub/software/unix/pftools/pft2.3/executables.
• The matrices required for the construction of generalized profiles: ftp://lausanne.isb-sib.ch/pub/software/unix/pftools/matrices.
• Older releases: ftp://lausanne.isb-sib.ch/pub/software/unix/pftools.

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Documentation | Downloads | pfsearchV3 | References | Contact

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pfsearchV3

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.

• Source code: ftp://lausanne.isb-sib.ch/pub/software/unix/pftools/pftoolsV3/pftoolsV3.tar.gz
• Pre-compiled executables: ftp://lausanne.isb-sib.ch/pub/software/unix/pftools/pftoolsV3/pftoolsV3.statics/
• PROSITE profiles calibrated for the heuristic: ftp://lausanne.isb-sib.ch/pub/software/unix/pftools/pftoolsV3/pftoolsV3.PROSITE.tar.gz

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Documentation | Downloads | pfsearchV3 | References | Contact

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References

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)

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Documentation | Downloads | pfsearchV3 | References | Contact

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Contact

Email the PROSITE team.