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Protein motif to search for Output section Output report format EMBL Genbank GFF PIR SwissProt EMBOSS list file DbMotif EMBOSS diffseq tabdelimited text EMBOSS FeatTable EMBOSS Motif EMBOSS Regions EMBOSS SeqTable SRS simple SRS EMBOSS Table EMBOSS tagseq.

EMBOSS: patmatdb

DescriptionInput File FormatOutput File FormatData FilesReferencesWarningsDiagnostic Error MessagesAuthorpatmatmotifs reads a protein sequence and searches it against the PROSITE database of motifs It writes a standard EMBOSS report file with details of the location and score of any matching motifs Optionally full documentation for matching patterns is given in the report Optionally simple posttranslational modification sites are not reported PROSITE must be processed by running prosextract before running patmatmotifs The home web page of PROSITE is http//wwwexpasych/prosite/ Quoting from the PROSITE user&#39s documentation In some cases the sequence of an unknown protein is too distantly related to any protein of known structure to detect its resemblance by overall sequence alignment but it can be identified by the occurrence in its sequence of a particular cluster of residue types which is variously known as a pattern motif signature or fingerprint These motifs arise because of particular requirements on the structure of specific region(s) of a protein which may be im The input is a standard EMBOSS sequence query (also known as a &#39USA&#39) Major sequence database sources defined as standard in EMBOSSinstallations include srsembl srsuniprot and ensembl Data can also be read from sequence output in any supported formatwritten by an EMBOSS or thirdparty application The input format can be specified by using thecommandline qualifier sformat xxx where &#39xxx&#39 is replacedby the name of the required format The available format names aregff (gff3) gff2 embl (em) genbank (gb refseq) ddbj refseqp pir(nbrf) swissprot (swiss sw) dasgff and debug Seehttp//embosssfnet/docs/themes/SequenceFormatshtmlfor further information on sequence formats The output is a standard EMBOSS report file The results can be output in one of several styles by using thecommandline qualifier rformat xxx where &#39xxx&#39 is replacedby the name of the required format The available format names areembl genbank gff pir swiss dasgff debug listfile dbmotifdiffseq draw restrict excel feattable motif nametable regionsseqtable simple srs table tagseq Seehttp//embosssfnet/docs/themes/ReportFormatshtmlfor further information on report formats By default patmatmotifswrites a &#39dbmotif&#39 report file Data and documentation from PROSITE files is automatically read This must be generated and formatted by running prosextract before running patmatmotifs Bairoch A Bucher P Hofmann K The PROSITE datatase its status in 1997 Nucleic Acids Res 24217221(1997) Other references 1 Bairoch A Bucher P (1994) PROSITE recent developments Nucleic Acids Research Vol 22 No17 35833589 2 Bairoch A (1992) PROSITE a dictionary of sites and patterns in proteins Nucleic Acids Research Vol 20 Supplement 20132018 3 Peek J O&#39Reilly T Loukides M (1997) Unix Power Tools 2nd Edition 4 Doolittle RF (In) Of URFs and ORFs a primer on how to analyzederived amino acid sequences University Science Books Mill ValleyCalifornia (1986) 5 Lesk AM (In) Computational Molecular Biology Lesk AM Edpp1726 Oxford University Press Oxford (1988) Your EMBOSS administrator must have set up the local EMBOSS PROSITE database using the utility prosextractbefore this program will run indicates that your local EMBOSS administrator has not yet correctlyset up the local EMBOSS PROSITE database using the utility &#39prosextract&#39 Please report all bugs to the EMBOSS bug team (embossbug © embossopenbioorg) not to the original author.

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