PFSEARCH(1) PFSEARCH(1) NAME pfsearch - search a protein or DNA sequence library for sequence segments matching a profile SYNOPSIS pfsearch [ -abflLrsuxyz ] [ profile-file | - ] [ seq-library-file | - ] [C=#] [W=#] DESCRIPTION pfsearch compares a query profile against a DNA or protein sequence library. The result is an unsorted list of pro- file-sequence matches written to the standard output. A variety of output formats containing different informa- tions can be specified via the options -a, -l, -L, -r, -u, -s, -x, -y, -z, and the command-line parameter C=#. pro- file-file contains a profile in PROSITE format. seq- library-file contains a sequence library in EMBL/SWISS- PROT format (assumed by default) or in Pearson/Fasta for- mat (indicated by option -f). pfsearch can be used as a filter if - is used instead of one of the input filenames. OPTIONS -a Report optimal alignment scores for all sequences regardless of the cut-off value. This option simultaneously forces DISJOINT=UNIQUE. -b Search the complementary strands of DNA sequences as well. -f Input sequence-library is in Pearson/Fasta format. -l Indicate by number the highest cut-off level exceeded by the match score in the output list. -L Indicate by character string the highest cut-off level exceeded by the match score in the output list. Note that the generalized profile format includes a text string field to specify a name for a cut-off level. The -L option causes the program to display the first two characters of this text string (usually something like "!", "?", "??", etc.) at the beginning of each match description. -r Use raw scores rather than normalized scores for match selection. Normalized scores will not be listed in the output. -s List the sequences of the matched regions as well. The output will be a Pearson/Fasta-formatted sequence library. -u Forces DISJOINT=UNIQUE. -x List profile-sequence alignments in pftools PSA format. -y Display alignments between the profile and the matched sequence regions in a human-friendly for- mat. -z Indicate starting and ending position of the matched profile range. The latter position will be given as a negative offset from the end of the pro- file. Thus the range [ 1, -1] means entire profile. PARAMETERS C=# Cut-off value. Over-writes the level zero cut-off value specified in the profile. An integer argu- ment is interpreted as a raw score value, a decimal argument as a normalized score value. An integer value forces option -r. W=# Output width. Output lines will be truncated after W characters. Default: W=132. EXAMPLES (1) pfsearch -f sh3.prf sh3.seq C=6.0 Searches the Pearson/Fasta-formatted protein sequence library sh3.seq for SH3 domains with a cut-off value of 6.0 normalized score units. sh3.seq contains 20 SH3 domain-containing protein sequences from SWISS-PROT release 32. sh3.prf con- tains the PROSITE entry SH3/PS50002. (2) pfsearch -bx ecp.prf CVPBR322 | psa2msa -du | read- seq -p -fMSF > ecp.msf Generates a multiple sequence alignment of poten- tial E. coli promoters on both strands of plasmid pBR322. ecp.prf contains a profile for E. coli promoters. CVPBR322 contains EMBL entry J01749|CVPBR322. The result file ecp.msf can fur- ther be processed by GCG programs accepting MSF files as input. See also manual pages of psa2msa. AUTHOR Philipp Bucher Philipp.Bucher@isrec.unil.ch PSA2MSA(1) PSA2MSA(1) NAME psa2msa - reformat PSA file to Pearson/Fasta multiple sequence alignment file SYNOPSIS psa2msa [ -dlpu ] [ [ psa-file | - ] ] [ M=#] DESCRIPTION psa2msa reformats a PSA-formatted profile-sequence align- ment file into a Pearson/Fasta-formatted multiple sequence alignment file. The result is written to the standard output. psa-file contains alignments of several sequence segments to the same profile in PSA format. Such a file is typically generated by program pfsearch using option -x. The output can be converted into other formats ( e.g. MSF) with the aid of the public domain program readseq (available from ftp.bio.indiana.edu:/molbio/readseq). psa2msa can be used as a filter if - is used instead of the input filename, or if the input filename is omitted. OPTIONS -d Replace periods by dashes on output. -l Replace upper case letters by lower case letters on output. -p Replace dashes by periods on output. -u Replace lower case letters by upper case letters on output. PARAMETERS M=# Maximal length of an insertion. If the real length of an insertion exceeds this value, the excess num- ber of residues will be deleted from the center of the insertion. M=0 means no upper limit for the length of an insertion. Setting an insertion length limit helps to keep the resulting alignment at manageable size. Default: M=0. EXAMPLES (1) pfsearch -bx ecp.prf CVPBR322 | psa2msa -du | read- seq -p -fMSF > ecp.msf Generates a multiple sequence alignment of pre- dicted E. coli promoters on both strands of plasmid pBR322. ecp.prf contains a profile for E. coli promoters. CVPBR322 contains EMBL entry J01749|CVPBR322. The result in ecp.msf can further be processed by GCG programs accepting MSF files as input. See also manual pages of pfsearch. AUTHOR Philipp Bucher Philipp.Bucher@isrec.unil.ch pftools 2.2 June 1999 PSA2MSA(1)