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).