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pftools - build and search protein and DNA 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.
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.

pfscale

Fit parameters of an extreme-value distribution to a profile score list.

pfw

Weight sequences of a multiple sequence alignment to correct for
sampling bias.

Programs to search with generalized profiles

pfsearch / pfsearchV3

Search a protein or DNA sequence library for sequence segments matching
a profile (V3 is the new version of this tool).

pfscan

Scan a protein or DNA sequence with a profile library

Conversion programs

psa2msa

Reformat PSA file to Pearson/Fasta multiple sequence alignment file.

ptof

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

2ft

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

6ft

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

pfgtop

Convert a profile in GCG format into PROSITE format.

pfhtop

Convert a HMMER1 ASCII-formatted HMM into an equivalent PROSITE profile.

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).

3
Debian iconDebian 10.0
Debian iconDebian 9.0
Ubuntu iconUbuntu 17.10
Ubuntu iconUbuntu 18.04 LTS
Ubuntu iconUbuntu 18.10
Ubuntu iconUbuntu 19.04
Ubuntu iconUbuntu 19.10
DistributionVersionSincePackageInstalledPackager
Debian iconDebian 10.0 buster/maindeb3+dfsg-3Jan 12383 kiB1.17 MiB
Debian iconDebian 9.0 stretch-backports/maindeb3+dfsg-3~bpo9+1Jan 12384 kiB1.14 MiB
Ubuntu iconUbuntu 17.10 artful/universedeb3+dfsg-2build12017-11-10385 kiB1.12 MiB
Ubuntu iconUbuntu 18.04 LTS bionic/universedeb3+dfsg-2build12017-11-10385 kiB1.12 MiB
Ubuntu iconUbuntu 18.10 cosmic/universedeb3+dfsg-2build2Jan 14383 kiB1.17 MiB
Ubuntu iconUbuntu 19.04 disco/universedeb3+dfsg-3Jan 14383 kiB1.17 MiB
Ubuntu iconUbuntu 19.10 eoan/universedeb3+dfsg-3Jun 17383 kiB1.17 MiB

Manual pages

2ft(1)

2ft - 2-frame translation of a DNA sequence into protein

6ft(1)

6ft - 6-frame translation of a DNA sequence into protein

pfdump(1)

pfdump - dump tool of pftools package

pfgtop(1)

gtop - convert a profile in GCG format into PROSITE format

pfhtop(1)

htop - convert a HMMER ASCII-formatted HMM into an equivalent profile

pfmake(1)

pfmake - generate a profile from a multiple sequence alignment

pfscale(1)

pfscale - fit parameters of an extreme-value distribution to a profile score list

pfscan(1)

pfscan - scan a protein or DNA sequence with a profile library

pfsearch(1)

pfsearch - search protein and DNA generalized profiles (legacy)

pfsearchV2(1)

pfsearchV2 - search a protein or DNA sequence library for sequence segments matching a profile

pfsearchV3(1)

pfsearchV3 - search protein and DNA generalized profiles (version 3)

pfw(1)

pfw - print focused window

psa2msa(1)

psa2msa - reformat PSA file to Pearson/Fasta multiple sequence alignment file

ptof(1)

ptof - convert a protein profile into a frame-search profile

ptoh(1)

ptoh - converts a PROSITE-formatted profile into an approximately equivalent HMM

Latest updates

Debian 9.0 icon

Debian 9.0 stretch-backports/main: Version 3+dfsg-3~bpo9+1 reintroduced

Yesterday
  • Rebuild for stretch-backports.
Debian 9.0 icon

Debian 9.0 stretch-backports/main: Version 3+dfsg-3~bpo9+1 removed

Yesterday
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Ubuntu 19.10 eoan/universe: Version 3+dfsg-3 reintroduced

0 - 11:38
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  • debian/upsdtream/metadata:
    • Pointed out that there are no references in registries
    • yamllint cleanliness
    Andreas Tille
    • debhelper 11
    • Point Vcs fields to salsa.debian.org
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      • Respect DEB_BUILD_OPTIONS in override_dh_auto_test
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Ubuntu 19.10 icon

Ubuntu 19.10 eoan/universe: Version 3+dfsg-3 removed

0 - 09:47
Ubuntu 19.10 icon

Ubuntu 19.10 eoan/universe: Version 3+dfsg-3 reintroduced

0 - 05:11
Steffen Moeller
  • debian/upsdtream/metadata:
    • Pointed out that there are no references in registries
    • yamllint cleanliness
    Andreas Tille
    • debhelper 11
    • Point Vcs fields to salsa.debian.org
    • Standards-Version: 4.2.1
    • d/rules:
      • Respect DEB_BUILD_OPTIONS in override_dh_auto_test
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Ubuntu 19.10 icon

Ubuntu 19.10 eoan/universe: Version 3+dfsg-3 removed

0 - 02:46
Ubuntu 19.10 icon

Ubuntu 19.10 eoan/universe: Version 3+dfsg-3 reintroduced

0 - 17:54
Steffen Moeller
  • debian/upsdtream/metadata:
    • Pointed out that there are no references in registries
    • yamllint cleanliness
    Andreas Tille
    • debhelper 11
    • Point Vcs fields to salsa.debian.org
    • Standards-Version: 4.2.1
    • d/rules:
      • Respect DEB_BUILD_OPTIONS in override_dh_auto_test
      • Do not parse d/changelog
Ubuntu 19.10 icon

Ubuntu 19.10 eoan/universe: Version 3+dfsg-3 removed

0 - 17:03
Ubuntu 19.10 icon

Ubuntu 19.10 eoan/universe: Version 3+dfsg-3 reintroduced

0 - 14:57
Steffen Moeller
  • debian/upsdtream/metadata:
    • Pointed out that there are no references in registries
    • yamllint cleanliness
    Andreas Tille
    • debhelper 11
    • Point Vcs fields to salsa.debian.org
    • Standards-Version: 4.2.1
    • d/rules:
      • Respect DEB_BUILD_OPTIONS in override_dh_auto_test
      • Do not parse d/changelog
Ubuntu 19.10 icon

Ubuntu 19.10 eoan/universe: Version 3+dfsg-3 removed

0 - 14:33
Ubuntu 19.10 icon

Ubuntu 19.10 eoan/universe: Version 3+dfsg-3 reintroduced

Aug 01
Steffen Moeller
  • debian/upsdtream/metadata:
    • Pointed out that there are no references in registries
    • yamllint cleanliness
    Andreas Tille
    • debhelper 11
    • Point Vcs fields to salsa.debian.org
    • Standards-Version: 4.2.1
    • d/rules:
      • Respect DEB_BUILD_OPTIONS in override_dh_auto_test
      • Do not parse d/changelog
Ubuntu 19.10 icon

Ubuntu 19.10 eoan/universe: Version 3+dfsg-3 removed

Aug 01
Ubuntu 19.10 icon

Ubuntu 19.10 eoan/universe: Version 3+dfsg-3 reintroduced

Jul 18
Steffen Moeller
  • debian/upsdtream/metadata:
    • Pointed out that there are no references in registries
    • yamllint cleanliness
    Andreas Tille
    • debhelper 11
    • Point Vcs fields to salsa.debian.org
    • Standards-Version: 4.2.1
    • d/rules:
      • Respect DEB_BUILD_OPTIONS in override_dh_auto_test
      • Do not parse d/changelog
Ubuntu 19.10 icon

Ubuntu 19.10 eoan/universe: Version 3+dfsg-3 removed

Jul 18
Ubuntu 19.10 icon

Ubuntu 19.10 eoan/universe: Version 3+dfsg-3 reintroduced

Jul 18
Steffen Moeller
  • debian/upsdtream/metadata:
    • Pointed out that there are no references in registries
    • yamllint cleanliness
    Andreas Tille
    • debhelper 11
    • Point Vcs fields to salsa.debian.org
    • Standards-Version: 4.2.1
    • d/rules:
      • Respect DEB_BUILD_OPTIONS in override_dh_auto_test
      • Do not parse d/changelog
Ubuntu 19.10 icon

Ubuntu 19.10 eoan/universe: Version 3+dfsg-3 removed

Jul 18
Ubuntu 19.10 icon

Ubuntu 19.10 eoan/universe: Version 3+dfsg-3 reintroduced

Jul 18
Steffen Moeller
  • debian/upsdtream/metadata:
    • Pointed out that there are no references in registries
    • yamllint cleanliness
    Andreas Tille
    • debhelper 11
    • Point Vcs fields to salsa.debian.org
    • Standards-Version: 4.2.1
    • d/rules:
      • Respect DEB_BUILD_OPTIONS in override_dh_auto_test
      • Do not parse d/changelog
Ubuntu 19.10 icon

Ubuntu 19.10 eoan/universe: Version 3+dfsg-3 removed

Jul 18
Debian 9.0 icon

Debian 9.0 stretch-backports/main: Version 3+dfsg-3~bpo9+1 reintroduced

Jul 15
  • Rebuild for stretch-backports.
Debian 9.0 icon

Debian 9.0 stretch-backports/main: Version 3+dfsg-3~bpo9+1 removed

Jul 15
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