patmatdb Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Searches protein sequences with a sequence motif Description patmatdb searches the input protein sequences for the specified sequence motif. The output is a standard EMBOSS report file including the number of matches between the motif and each input sequence, length of match, start and end positions of match, and the motif-sequence alignment. Patterns for patmatdb are based on the format of pattern used in the PROSITE database, with the difference that the terminating dot '.' and the hyphens, '-', between the characters are optional. Algorithm Patterns for patmatdb are based on the format of pattern used in the PROSITE database, with the difference that the terminating dot '.' and the hyphens, '-', between the characters are optional. For example: [DE](2)HS{P}X(2)PX(2,4)C means two Asps or Glus in any order followed by His, Ser, any residue other then Pro, then two of any residue followed by Pro followed by two to four of any residue followed by Cys. The search is case-independent, so AAA matches aaa. (Any string of at least 2 characters). Usage Here is a sample session with patmatdb % patmatdb Searches protein sequences with a sequence motif Input protein sequence(s): tsw:* Protein motif to search for: st[ty]s Output report [12s1_arath.patmatdb]: ajSeqxrefNewDbS '1-I' 'FT025' Go to the input files for this example Go to the output files for this example Command line arguments Searches protein sequences with a sequence motif Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqall Protein sequence(s) filename and optional format, or reference (input USA) [-motif] string Patterns for patmatdb are based on the format of pattern used in the PROSITE database. For example: '[DE](2)HS{P}X(2)PX(2,4)C' means two Asps or Glus in any order followed by His, Ser, any residue other then Pro, then two of any residue followed by Pro followed by two to four of any residue followed by Cys. The search is case-independent, so 'AAA' matches 'aaa'. (Any string of at least 2 characters) [-outfile] report [*.patmatdb] Output report file name (default -rformat dbmotif) Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -sformat1 string Input sequence format -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outfile" associated qualifiers -rformat3 string Report format -rname3 string Base file name -rextension3 string File name extension -rdirectory3 string Output directory -raccshow3 boolean Show accession number in the report -rdesshow3 boolean Show description in the report -rscoreshow3 boolean Show the score in the report -rstrandshow3 boolean Show the nucleotide strand in the report -rusashow3 boolean Show the full USA in the report -rmaxall3 integer Maximum total hits to report -rmaxseq3 integer Maximum hits to report for one sequence General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Input file format patmatdb reads in one or more protein sequences. The input is a standard EMBOSS sequence query (also known as a 'USA'). Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application. The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug. See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats. Input files for usage example 'tsw:*' is a sequence entry in the example protein database 'tsw' Pattern specification Patterns for patmatdb are based on the format of pattern used in the PROSITE database, with the difference that the terminating dot '.' and the hyphens, '-', between the characters are optional. The PROSITE pattern definition from the PROSITE documentation follows. * The standard IUPAC one-letter codes for the amino acids are used. * The symbol `x' is used for a position where any amino acid is accepted. * Ambiguities are indicated by listing the acceptable amino acids for a given position, between square parentheses `[ ]'. For example: [ALT] stands for Ala or Leu or Thr. * Ambiguities are also indicated by listing between a pair of curly brackets `{ }' the amino acids that are not accepted at a given position. For example: {AM} stands for any amino acid except Ala and Met. * Each element in a pattern is separated from its neighbor by a `-'. (Optional in patmatdb). * Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical range between parenthesis. Examples: x(3) corresponds to x-x-x, x(2,4) corresponds to x-x or x-x-x or x-x-x-x. * When a pattern is restricted to either the N- or C-terminal of a sequence, that pattern either starts with a `<' symbol or respectively ends with a `>' symbol. * A period ends the pattern. (Optional in patmatdb). For example, in SWISSPROT entry 100K_RAT you can look for the pattern: [DE](2)HS{P}X(2)PX(2,4)C This means: Two Asps or Glus in any order followed by His, Ser, any residue other then Pro, then two of any residue followed by Pro followed by two to four of any residue followed by Cys. The search is case-independent, so 'AAA' matches 'aaa'. Output file format The output is a standard EMBOSS report file. The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, draw, restrict, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq. See: http://emboss.sf.net/docs/themes/ReportFormats.html for further information on report formats. By default the output is in 'dbmotif' format. Output files for usage example File: 12s1_arath.patmatdb ######################################## # Program: patmatdb # Rundate: Fri 15 Jul 2011 12:00:00 # Commandline: patmatdb # -sequence "tsw:*" # -motif "st[ty]s" # Report_format: dbmotif # Report_file: 12s1_arath.patmatdb ######################################## #======================================= # # Sequence: GCN4_YEAST from: 1 to: 281 # HitCount: 1 # # Motif: ST[TY]S # #======================================= Length = 4 Start = position 158 of sequence End = position 161 of sequence SNLEVSTTSFLPTP | | 158 161 #--------------------------------------- #--------------------------------------- #======================================= # # Sequence: HD_TAKRU from: 1 to: 3148 # HitCount: 1 # # Motif: ST[TY]S # #======================================= Length = 4 Start = position 1038 of sequence End = position 1041 of sequence STPASSTTSSAVDP | | 1038 1041 #--------------------------------------- #--------------------------------------- #======================================= # # Sequence: PAXI_HUMAN from: 1 to: 591 # HitCount: 1 # # Motif: ST[TY]S # #======================================= Length = 4 Start = position 13 of sequence End = position 16 of sequence LADLESTTSHISKR | | 13 16 #--------------------------------------- #--------------------------------------- #--------------------------------------- # Total_sequences: 100 # Total_length: 35357 # Reported_sequences: 3 # Reported_hitcount: 3 #--------------------------------------- Data files None. Notes None. References 1. Bairoch, A., Bucher P. (1994) PROSITE: recent developments. Nucleic Acids Research, Vol 22, No.17 3583-3589. 2. Bairoch, A., (1992) PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Research, Vol 20, Supplement, 2013-2018. 3. Peek, J., O'Reilly, T., Loukides, M., (1997) Unix Power Tools, 2nd Edition. 4. Gusfield, D., (1997) Algorithms on strings, Trees and Sequences. 5. Sedgewick, R,. (1990) Algorithms in C. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0 Known bugs None. See also Program name Description antigenic Finds antigenic sites in proteins epestfind Finds PEST motifs as potential proteolytic cleavage sites fuzzpro Search for patterns in protein sequences fuzztran Search for patterns in protein sequences (translated) patmatmotifs Scan a protein sequence with motifs from the PROSITE database preg Regular expression search of protein sequence(s) pscan Scans protein sequence(s) with fingerprints from the PRINTS database sigcleave Reports on signal cleavage sites in a protein sequence Author(s) Sinead O'Leary formerly at: HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Completed April 30 1999. Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None