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
pfsearch / pfsearchV3
Search a protein or DNA sequence library for sequence segments matching
a profile (V3 is the new version of this tool).
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).
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Install this software package
If the package is available for the distribution you are currently using on your computer then install the software by clicking on… Install pftools