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<HEAD>
  <TITLE>
  EMBOSS: patmatmotifs
  </TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">

<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
patmatmotifs
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
    Function
</H2>
Search a PROSITE motif database with a protein sequence

<H2>
    Description
</H2>


<b>patmatmotifs</b> takes a protein sequence and compares it to the
PROSITE database of motifs. 

<p>

For a description of PROSITE, we can do no better than to quote the
PROSITE user's documentation:

<i>
<p>
   PROSITE is a method of determining what is the function of uncharacterized
   proteins translated  from genomic  or cDNA  sequences. It  consists  of  a
   database of biologically significant sites and patterns formulated in such
   a way  that with  appropriate  computational  tools  it  can  rapidly  and
   reliably identify  to which  known family  of protein  (if  any)  the  new
   sequence belongs.

<p>
   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 important, for example, for their binding properties
   or for  their enzymatic  activity. These  requirements impose  very  tight
   constraints on  the evolution  of those  limited (in  size) but  important
   portion(s) of a protein sequence. To paraphrase Orwell, in Animal Farm, we
   can say  that "some  regions of  a protein  sequence are  more equal  than
   others" !

<p>
   The use  of  protein  sequence  patterns  (or  motifs)  to  determine  the
   function(s) of  proteins is  becoming very  rapidly one  of the  essential
   tools of  sequence analysis.  This reality  has been  recognized  by  many
   authors, as it can be illustrated from the following citations from two of
   the most  well known  experts of protein sequence analysis, R.F. Doolittle
   and A.M. Lesk:

<pre>
      "There are  many short  sequences  that  are  often  (but  not  always)
      diagnostics of certain binding properties or active sites. These can be
      set into a small subcollection and searched against your sequence (1)".

      "In some  cases, the structure and function of an unknown protein which
      is too  distantly related  to any  protein of known structure to detect
      its affinity  by overall  sequence alignment  may be  identified by its
      possession of  a particular  cluster of  residues types classified as a
      motifs. The  motifs, or  templates, or  fingerprints, arise  because of
      particular  requirements  of  binding  sites  that  impose  very  tight
      constraint on the evolution of portions of a protein sequence (2)."
</pre>
</i>

<p>
The home web page of PROSITE is: <a
href="http://www.expasy.ch/prosite/">http://www.expasy.ch/prosite/</a>

<p>

It is common to find that a search of the PROSITE database against a
protein sequence will report many matches to the short motifs that are
indicative of the post-translational modification sites, such as
glycolsylation, myristylation and phosphorylation sites.  These reports
are often unwanted and are not normally reported.  You can turn
reporting of these short motifs on by giving the '-noprune' option on
the command-line. 

<p>

Your EMBOSS administrator must have set up the local EMBOSS PROSITE
database using the utility '<b>prosextract</b>' before this program will run. 

<H2>
    Usage
</H2>
<b>Here is a sample session with patmatmotifs</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>patmatmotifs -full </b>
Search a PROSITE motif database with a protein sequence
Input protein sequence: <b>tsw:opsd_human</b>
Output report [opsd_human.patmatmotifs]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>


<H2>
    Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   Protein sequence filename and optional
                                  format, or reference (input USA)
  [-outfile]           report     [*.patmatmotifs] Output report file name

   Additional (Optional) qualifiers:
   -full               boolean    [N] Provide full documentation for matching
                                  patterns
   -[no]prune          boolean    [Y] Ignore simple patterns. If this is true
                                  then these simple post-translational
                                  modification sites are not reported:
                                  myristyl, asn_glycosylation,
                                  camp_phospho_site, pkc_phospho_site,
                                  ck2_phospho_site, and tyr_phospho_site.

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the 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
   -rformat2           string     Report format
   -rname2             string     Base file name
   -rextension2        string     File name extension
   -rdirectory2        string     Output directory
   -raccshow2          boolean    Show accession number in the report
   -rdesshow2          boolean    Show description in the report
   -rscoreshow2        boolean    Show the score in the report
   -rusashow2          boolean    Show the full USA in the report
   -rmaxall2           integer    Maximum total hits to report
   -rmaxseq2           integer    Maximum hits to report for one sequence

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write 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. 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

</pre>
</td></tr></table>
<P>

<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td>[-sequence]<br>(Parameter 1)</td>
<td>Protein sequence filename and optional format, or reference (input USA)</td>
<td>Readable sequence</td>
<td><b>Required</b></td>
</tr>

<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>Output report file name</td>
<td>Report output file</td>
<td><i>&lt;*&gt;</i>.patmatmotifs</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td>-full</td>
<td>Provide full documentation for matching patterns</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr>
<td>-[no]prune</td>
<td>Ignore simple patterns. If this is true then these simple post-translational modification sites are not reported: myristyl, asn_glycosylation, camp_phospho_site, pkc_phospho_site, ck2_phospho_site, and tyr_phospho_site.</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td colspan=4>(none)</td>
</tr>

</table>


<H2>
    Input file format
</H2>


<b>patmatmotifs</b> reads a protein sequence USA.

<p>


<a name="input.1"></a>
<h3>Input files for usage example </h3>

'tsw:opsd_human' is a sequence entry in the example protein database 'tsw'
<p>
<p><h3>Database entry: tsw:opsd_human</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
ID   OPSD_HUMAN              Reviewed;         348 AA.
AC   P08100; Q16414; Q2M249;
DT   01-AUG-1988, integrated into UniProtKB/Swiss-Prot.
DT   01-AUG-1988, sequence version 1.
DT   20-MAR-2007, entry version 91.
DE   Rhodopsin (Opsin-2).
GN   Name=RHO; Synonyms=OPN2;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC   Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   MEDLINE=84272729; PubMed=6589631;
RA   Nathans J., Hogness D.S.;
RT   "Isolation and nucleotide sequence of the gene encoding human
RT   rhodopsin.";
RL   Proc. Natl. Acad. Sci. U.S.A. 81:4851-4855(1984).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA   Suwa M., Sato T., Okouchi I., Arita M., Futami K., Matsumoto S.,
RA   Tsutsumi S., Aburatani H., Asai K., Akiyama Y.;
RT   "Genome-wide discovery and analysis of human seven transmembrane helix
RT   receptor genes.";
RL   Submitted (JUL-2001) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   TISSUE=Retina;
RG   The German cDNA consortium;
RL   Submitted (JUN-2003) to the EMBL/GenBank/DDBJ databases.
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX   PubMed=15489334; DOI=10.1101/gr.2596504;
RG   The MGC Project Team;
RT   "The status, quality, and expansion of the NIH full-length cDNA
RT   project: the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-120.
RX   PubMed=8566799; DOI=10.1016/0378-1119(95)00688-5;
RA   Bennett J., Beller B., Sun D., Kariko K.;
RT   "Sequence analysis of the 5.34-kb 5' flanking region of the human
RT   rhodopsin-encoding gene.";
RL   Gene 167:317-320(1995).
RN   [6]
RP   REVIEW ON RP4 VARIANTS.
RX   MEDLINE=94004905; PubMed=8401533;
RA   Al-Maghtheh M., Gregory C., Inglehearn C., Hardcastle A.,
RA   Bhattacharya S.;


<font color=red>  [Part of this file has been deleted for brevity]</font>

FT                                /FTId=VAR_004816.
FT   VARIANT     209    209       V -&gt; M (effect not known).
FT                                /FTId=VAR_004817.
FT   VARIANT     211    211       H -&gt; P (in RP4).
FT                                /FTId=VAR_004818.
FT   VARIANT     211    211       H -&gt; R (in RP4).
FT                                /FTId=VAR_004819.
FT   VARIANT     216    216       M -&gt; K (in RP4).
FT                                /FTId=VAR_004820.
FT   VARIANT     220    220       F -&gt; C (in RP4).
FT                                /FTId=VAR_004821.
FT   VARIANT     222    222       C -&gt; R (in RP4).
FT                                /FTId=VAR_004822.
FT   VARIANT     255    255       Missing (in RP4).
FT                                /FTId=VAR_004823.
FT   VARIANT     264    264       Missing (in RP4).
FT                                /FTId=VAR_004824.
FT   VARIANT     267    267       P -&gt; L (in RP4).
FT                                /FTId=VAR_004825.
FT   VARIANT     267    267       P -&gt; R (in RP4).
FT                                /FTId=VAR_004826.
FT   VARIANT     292    292       A -&gt; E (in CSNBAD1).
FT                                /FTId=VAR_004827.
FT   VARIANT     296    296       K -&gt; E (in RP4).
FT                                /FTId=VAR_004828.
FT   VARIANT     297    297       S -&gt; R (in RP4).
FT                                /FTId=VAR_004829.
FT   VARIANT     342    342       T -&gt; M (in RP4).
FT                                /FTId=VAR_004830.
FT   VARIANT     345    345       V -&gt; L (in RP4).
FT                                /FTId=VAR_004831.
FT   VARIANT     345    345       V -&gt; M (in RP4).
FT                                /FTId=VAR_004832.
FT   VARIANT     347    347       P -&gt; A (in RP4).
FT                                /FTId=VAR_004833.
FT   VARIANT     347    347       P -&gt; L (in RP4; common variant).
FT                                /FTId=VAR_004834.
FT   VARIANT     347    347       P -&gt; Q (in RP4).
FT                                /FTId=VAR_004835.
FT   VARIANT     347    347       P -&gt; R (in RP4).
FT                                /FTId=VAR_004836.
FT   VARIANT     347    347       P -&gt; S (in RP4).
FT                                /FTId=VAR_004837.
SQ   SEQUENCE   348 AA;  38893 MW;  6F4F6FCBA34265B2 CRC64;
     MNGTEGPNFY VPFSNATGVV RSPFEYPQYY LAEPWQFSML AAYMFLLIVL GFPINFLTLY
     VTVQHKKLRT PLNYILLNLA VADLFMVLGG FTSTLYTSLH GYFVFGPTGC NLEGFFATLG
     GEIALWSLVV LAIERYVVVC KPMSNFRFGE NHAIMGVAFT WVMALACAAP PLAGWSRYIP
     EGLQCSCGID YYTLKPEVNN ESFVIYMFVV HFTIPMIIIF FCYGQLVFTV KEAAAQQQES
     ATTQKAEKEV TRMVIIMVIA FLICWVPYAS VAFYIFTHQG SNFGPIFMTI PAFFAKSAAI
     YNPVIYIMMN KQFRNCMLTT ICCGKNPLGD DEASATVSKT ETSQVAPA
//
</pre>
</td></tr></table><p>

<H2>
    Output file format
</H2>


<p>

The output is a standard EMBOSS report file. 

<p>

The results can be output in one of several styles by using the
command-line qualifier <b>-rformat xxx</b>, where 'xxx' is replaced by
the name of the required format.  The available format names are: embl,
genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel,
feattable, motif, regions, seqtable, simple, srs, table, tagseq

<p>

See:
<A href="http://emboss.sf.net/docs/themes/ReportFormats.html">
http://emboss.sf.net/docs/themes/ReportFormats.html</A>
for further information on report formats.

<p>

<p>

By default <b>patmatmotifs</b> writes a 'dbmotif' report file.

<p>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: opsd_human.patmatmotifs</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
########################################
# Program: patmatmotifs
# Rundate: Sun 15 Jul 2007 12:00:00
# Commandline: patmatmotifs
#    -full
#    -sequence tsw:opsd_human
# Report_format: dbmotif
# Report_file: opsd_human.patmatmotifs
########################################

#=======================================
#
# Sequence: OPSD_HUMAN     from: 1   to: 348
# HitCount: 2
#
# Full: Yes
# Prune: Yes
# Data_file: ../prosextract-keep/PROSITE/prosite.lines
#
#=======================================

Length = 17
Start = position 123 of sequence
End = position 139 of sequence

Motif = G_PROTEIN_RECEP_F1_1

TLGGEIALWSLVVLAIERYVVVCKPMS
     |               |
   123               139

Length = 17
Start = position 290 of sequence
End = position 306 of sequence

Motif = OPSIN

PIFMTIPAFFAKSAAIYNPVIYIMMNK
     |               |
   290               306


#---------------------------------------
#
# Motif: G_PROTEIN_RECEP_F1_1
# Count: 1
# 
# *****************************************
# * G-protein coupled receptors signature *
# *****************************************


<font color=red>  [Part of this file has been deleted for brevity]</font>

# Count: 1
# 
# *************************************************
# * Visual pigments (opsins) retinal binding site *
# *************************************************
# 
# Visual pigments [1,2] are the light-absorbing  molecules that  mediate vision.
# They consist of  an apoprotein, opsin,  covalently  linked  to the chromophore
# cis-retinal.  Vision is  effected through  the absorption of a  photon by cis-
# retinal  which is isomerized to  trans-retinal.  This isomerization leads to a
# change  of conformation  of the protein. Opsins are integral membrane proteins
# with  seven transmembrane regions that belong to family 1 of G-protein coupled
# receptors (see &lt;PDOC00210&gt;).
# 
# In vertebrates four different pigments are generally found.   Rod cells, which
# mediate vision in dim light, contain the pigment rhodopsin.  Cone cells, which
# function in bright light, are responsible  for  color vision and contain three
# or more color pigments (for example, in mammals: red, blue and green).
# 
# In Drosophila, the  eye   is composed   of 800   facets  or   ommatidia.  Each
# ommatidium contains eight photoreceptor cells (R1-R8):  the R1 to R6 cells are
# outer cells,  R7  and R8 inner cells. Each of the three types of cells (R1-R6,
# R7 and R8) expresses a specific opsin.
# 
# Proteins evolutionary related to opsins include squid retinochrome, also known
# as retinal  photoisomerase, which converts various isomers of retinal into 11-
# cis retinal and mammalian retinal pigment  epithelium (RPE) RGR [3], a protein
# that may also act in retinal isomerization.
# 
# The attachment  site  for  retinal in the above proteins is a conserved lysine
# residue in  the  middle  of  the  seventh  transmembrane helix. The pattern we
# developed includes this residue.
# 
# -Consensus pattern: [LIVMWAC]-[PGAC]-x(3)-[SAC]-K-[STALIMR]-[GSACPNV]-[STACP]-
#                     x(2)-[DENF]-[AP]-x(2)-[IY]
#                     [K is the retinal binding site]
# -Sequences known to belong to this class detected by the pattern: ALL.
# -Other sequence(s) detected in SWISS-PROT: NONE.
# -Last update: July 1998 / Pattern and text revised.
# 
# [ 1] Applebury M.L., Hargrave P.A.
#      Vision Res. 26:1881-1895(1986).
# [ 2] Fryxell K.J., Meyerowitz E.M.
#      J. Mol. Evol. 33:367-378(1991).
# [ 3] Shen D., Jiang M., Hao W., Tao L., Salazar M., Fong H.K.W.
#      Biochemistry 33:13117-13125(1994).
# 
# ***************
# 
#
#---------------------------------------
</pre>
</td></tr></table><p>


<H2>
    Data files
</H2>


Data and documentation from PROSITE files is automatically read. This
has been generated and formatted by running <b>prosextract</b> before running
<b>patmatmotifs</b>.

<H2>
    Notes
</H2>


Program is only useful when <b>prosextract</b> is used beforehand.  

<H2>
    References
</H2>


If you want to refer to PROSITE in a publication you can do so by citing:

<p>
      Bairoch A., Bucher P., Hofmann K.
      The PROSITE datatase, its status in 1997.
      Nucleic Acids Res. 24:217-221(1997).

<p>

Other references:

<p>
<ol>
<li>Bairoch, A., Bucher P. (1994) PROSITE: recent developments. Nucleic 
Acids Research, Vol 22, No.17 3583-3589.

<li>Bairoch, A., (1992) PROSITE: a dictionary of sites and patterns in 
proteins. Nucleic Acids Research, Vol 20, Supplement, 2013-2018.

<li>Peek, J., O'Reilly, T., Loukides, M., (1997) Unix Power Tools, 2nd 
Edition.

<li>Doolittle R.F.  (In) Of URFs and ORFs: a primer on how to analyze
derived amino acid sequences., University Science Books, Mill Valley,
California, (1986).

<li>Lesk A.M.  (In) Computational Molecular Biology, Lesk A.M., Ed.,
pp17-26, Oxford University Press, Oxford (1988).

</ol>

<H2>
    Warnings
</H2>


Your EMBOSS administrator must have set up the local EMBOSS PROSITE
database using the utility '<b>prosextract</b>' before this program will run.

<H2>
    Diagnostic Error Messages
</H2>


The error message: 

<p>

<pre>
"Either EMBOSS_DATA undefined or PROSEXTRACT needs running"
</pre>

<p>

indicates that your local EMBOSS administrator has not yet correctly
set up the local EMBOSS PROSITE database using the utility <a
href="prosextract.html">'prosextract'.</a>

<H2>
    Exit status
</H2>


It always exits with status 0

<H2>
    Known bugs
</H2>

None.

<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="antigenic.html">antigenic</a></td>
<td>Finds antigenic sites in proteins</td>
</tr>

<tr>
<td><a href="digest.html">digest</a></td>
<td>Protein proteolytic enzyme or reagent cleavage digest</td>
</tr>

<tr>
<td><a href="epestfind.html">epestfind</a></td>
<td>Finds PEST motifs as potential proteolytic cleavage sites</td>
</tr>

<tr>
<td><a href="fuzzpro.html">fuzzpro</a></td>
<td>Protein pattern search</td>
</tr>

<tr>
<td><a href="fuzztran.html">fuzztran</a></td>
<td>Protein pattern search after translation</td>
</tr>

<tr>
<td><a href="helixturnhelix.html">helixturnhelix</a></td>
<td>Report nucleic acid binding motifs</td>
</tr>

<tr>
<td><a href="oddcomp.html">oddcomp</a></td>
<td>Find protein sequence regions with a biased composition</td>
</tr>

<tr>
<td><a href="patmatdb.html">patmatdb</a></td>
<td>Search a protein sequence with a motif</td>
</tr>

<tr>
<td><a href="pepcoil.html">pepcoil</a></td>
<td>Predicts coiled coil regions</td>
</tr>

<tr>
<td><a href="preg.html">preg</a></td>
<td>Regular expression search of a protein sequence</td>
</tr>

<tr>
<td><a href="pscan.html">pscan</a></td>
<td>Scans proteins using PRINTS</td>
</tr>

<tr>
<td><a href="sigcleave.html">sigcleave</a></td>
<td>Reports protein signal cleavage sites</td>
</tr>

</table>

<H2>
    Author(s)
</H2>


Sinead O'Leary (current e-mail address unknown)
<br>
while she was at:
<br>
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK



<H2>
    History
</H2>


Completed May 13 1999.

<H2>
    Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.

<H2>
    Comments
</H2>
None

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