Bug#859196: ITP: pftools -- build and search protein and DNA generalized profiles
- Date: Fri, 31 Mar 2017 13:46:48 +0200
- From: Andreas Tille <tille@xxxxxxxxxx>
- Subject: Bug#859196: ITP: pftools -- build and search protein and DNA generalized profiles
Owner: Andreas Tille <tille@xxxxxxxxxx>
* Package name : pftools
Version : 3
Upstream Author : Alan Bridge, Christian Sigrist, Gregoire Rossier
* URL : http://web.expasy.org/pftools/
* License : GPL
Programming Lang: C
Description : 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
Build a profile from a multiple sequence alignment.
Fit parameters of an extreme-value distribution to a profile score list.
Weight sequences of a multiple sequence alignment to correct for
Programs to search with generalized profiles
Search a protein or DNA sequence library for sequence segments matching
Scan a protein or DNA sequence with a profile library
Reformat PSA file to Pearson/Fasta multiple sequence alignment file.
Convert a protein profile into a frame-search profile to search DNA
sequences. To be used with 2ft.
Converts both strands of DNA into so-called interleaved
frame-translated DNA sequences to search with protein profiles. To be
used with ptof.
Translates all six reading frames of a double-stranded DNA sequence
into individual protein sequences.
Convert a profile in GCG format into PROSITE format.
Convert a HMMER1 ASCII-formatted HMM into an equivalent PROSITE profile.
Converts a generalized profile into an approximately equivalent HMM
profile in HMMER1 format (can be read by the hmmconvert program from
the HMMER2 package).
Remark: This package will be maintained by the Debian Med team at