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).