]> 2.2 Profile Tools P. Bucher Bucher P, Karplus K, Moeri N and Hofmann, K. (1996). A flexible motif search technique based on generalized profiles. Comput. Chem. 20:3-24. nucleic:profiles protein:profiles profiles pftools pftools PFTOOLS program perl "| $value " pfscan 2 pfscan pfscan: scan a sequence with a profile db pfsearch pfsearch: search a sequence db for segments matching a profile pfscan compares a protein or nucleic acid sequence against a profile library (default: Prosite). pfsearch compares a query profile against a DNA or protein sequence library. The result is an unsorted list of profile-sequence matches written to the standard output. clean_output perl " | clean_pfscan_output " 10000 perl $pftools eq "pfscan" fastaformat perl " -f" 3 pfscan PFSCAN parameters perl ($pftools eq "pfscan") seqfile Sequence File perl "cat $value " 1 pfscan will scan this sequence with a profile db (default db: PROSITE) 8 perl ($pftools eq "pfscan") prosite Scan PROSITE db (default)? perl ($value)? " /local/gensoft/lib/pftools/db/prosite.dat" : "" 1 6 perl ($pftools eq "pfscan") profiledb Profile db (PROSITE/NUCSITE format) (if not PROSITE) perl $value 6 perl ($pftools eq "pfscan") && ( ! $prosite ) pfscan_cutoff Cut-off value perl (defined $value)? " L=$value":"" 7 Cut-off level to be used for match selection. If level L is not specified in the profile, the next higher (if L is negative) or next lower (if L is positive) level specified is used instead. perl ($pftools eq "pfscan") pfsearch PFSEARCH parameters perl ($pftools eq "pfsearch") profile Profile File (PROSITE/NUCSITE format, or see next option) perl ($gcg2psa)? "gtop $value" : "cat $value" 1 perl ($pftools eq "pfsearch") gcg_profile perl 1 gcg2psa Convert the profile from GCG format to PROSITE format ? perl "" 1 perl ($pftools eq "pfsearch") aa_or_nuc_db protein or nucleotid db perl "" protein protein protein dna DNA perl ($pftools eq "pfsearch") aadb Protein Database perl " /local/gensoft/lib/fasta/db/$value" uniprot 6 &protdbs; You must either choose a protein or a nucleotid db perl ! (defined $aadb || defined $nucdb) perl ($pftools eq "pfsearch") && ($aa_or_nuc_db eq "protein") nucdb Nucleotid Database perl " /local/gensoft/lib/fasta/db/$value" genbank 6 &nucdbs; perl ($pftools eq "pfsearch") && ($aa_or_nuc_db eq "dna") pfsearch_cutoff Cut-off value perl (defined $value)? " C=$value":"" 7 Over-writes the level zero cut-off value specified in the profile. An integer argument is interpreted as a raw score value, a decimal argument as a normalized score value. perl ($pftools eq "pfsearch") psa2msa reformat PSA result file to Fasta multiple sequence alignment file? perl ($value)? " | psa2msa - " : "" 1 8 perl ($pftools eq "pfsearch") stdinput perl " - " 5 control Control options compl Search the complementary strands of DNA sequences as well (-b) perl ($value)? " -b":"" 4 raw_score Use raw scores rather than normalized scores for match selection. Normalized scores will not be listed in the output. (-r) perl ($value)? " -r":"" 4 unique Forces DISJOINT=UNIQUE (-u) perl ($value)? " -u":"" 4 output Output options optimal Report optimal alignment scores for all sequences regardless of the cut-off value (-a)? perl ($value)? " -a":"" 4 This option simultaneously forces DISJOINT=UNIQUE. listseq List the sequences of the matched regions as well. The output will be a Pearson/Fasta-formatted sequence library. (-s) perl ($value)? " -s":"" 4 psa_format List profile-sequence alignments in pftools PSA format. (-x) perl ($value)? " -x":"" 4 between Display alignments between the profile and the matched sequence regions in a human-friendly format. (-y) perl ($value)? " -y":"" 4