Paketti: pftools (3.2.11-2)

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).