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<HEAD>
  <TITLE>
  EMBOSS: prophecy
  </TITLE>
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<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="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
prophecy
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Create frequency matrix or profile from a multiple alignment

<H2>
    Description
</H2>

<p>prophecy generates for an input sequence alignment a simple frequency matrix (for use by profit) or a position specific weighted profile using either the Gribskov (1) or Henikoff (2) method (for use by prophet). For constructing a simple frequency matrix, a residue substitution matrix, gap opening and gap extension penalty must be specified.</p>



<h2>Algorithm</h2>

<p>The Gribskov scoring scheme is based on a notion of distance between a sequence and an ancestral or generalized sequence. For Henikoff it is based on weights of the diversity observed at each position in the alignment, rather than on a sequence distance measure.</p>



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

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

% <b>prophecy </b>
Create frequency matrix or profile from a multiple alignment
Input (aligned) sequence set: <b>globins.msf</b>
Profile type
         F : Frequency
         G : Gribskov
         H : Henikoff
Select type [F]: <b></b>
Enter a name for the profile [mymatrix]: <b>globins</b>
Enter threshold reporting percentage [75]: <b></b>
Output file [globins.prophecy]: <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>
<p>
<b>Example 2</b>
<p>

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

% <b>prophecy </b>
Create frequency matrix or profile from a multiple alignment
Input (aligned) sequence set: <b>globins.msf</b>
Profile type
         F : Frequency
         G : Gribskov
         H : Henikoff
Select type [F]: <b>g</b>
Scoring matrix [Epprofile]: <b></b>
Enter a name for the profile [mymatrix]: <b>globins</b>
Gap opening penalty [3.0]: <b></b>
Gap extension penalty [0.3]: <b></b>
Output file [globins.prophecy]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#output.2">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>
Create frequency matrix or profile from a multiple alignment
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqset     (Aligned) sequence set filename and optional
                                  format, or reference (input USA)
   -type               menu       [F] Select type (Values: F (Frequency); G
                                  (Gribskov); H (Henikoff))
*  -datafile           matrixf    ['Epprofile' for Gribskov type, or
                                  EBLOSUM62] Scoring matrix
   -name               string     [mymatrix] Enter a name for the profile (Any
                                  string)
*  -threshold          integer    [75] Enter threshold reporting percentage
                                  (Integer from 1 to 100)
*  -open               float      [3.0] Gap opening penalty (Any numeric
                                  value)
*  -extension          float      [0.3] Gap extension penalty (Any numeric
                                  value)
  [-outfile]           outfile    [*.prophecy] Output file name

   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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   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

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

<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-sequence]<br>(Parameter 1)</td>
<td>seqset</td>
<td>(Aligned) sequence set filename and optional format, or reference (input USA)</td>
<td>Readable set of sequences</td>
<td><b>Required</b></td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-type</td>
<td>list</td>
<td>Select type</td>
<td><table><tr><td>F</td> <td><i>(Frequency)</i></td></tr><tr><td>G</td> <td><i>(Gribskov)</i></td></tr><tr><td>H</td> <td><i>(Henikoff)</i></td></tr></table></td>
<td>F</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-datafile</td>
<td>matrixf</td>
<td>Scoring matrix</td>
<td>Comparison matrix file in EMBOSS data path</td>
<td>'Epprofile' for Gribskov type, or EBLOSUM62</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-name</td>
<td>string</td>
<td>Enter a name for the profile</td>
<td>Any string</td>
<td>mymatrix</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-threshold</td>
<td>integer</td>
<td>Enter threshold reporting percentage</td>
<td>Integer from 1 to 100</td>
<td>75</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-open</td>
<td>float</td>
<td>Gap opening penalty</td>
<td>Any numeric value</td>
<td>3.0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-extension</td>
<td>float</td>
<td>Gap extension penalty</td>
<td>Any numeric value</td>
<td>0.3</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-outfile]<br>(Parameter 2)</td>
<td>outfile</td>
<td>Output file name</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.prophecy</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-sequence" associated seqset qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sbegin1<br>-sbegin_sequence</td>
<td>integer</td>
<td>Start of each sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -send1<br>-send_sequence</td>
<td>integer</td>
<td>End of each sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sreverse1<br>-sreverse_sequence</td>
<td>boolean</td>
<td>Reverse (if DNA)</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sask1<br>-sask_sequence</td>
<td>boolean</td>
<td>Ask for begin/end/reverse</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -snucleotide1<br>-snucleotide_sequence</td>
<td>boolean</td>
<td>Sequence is nucleotide</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sprotein1<br>-sprotein_sequence</td>
<td>boolean</td>
<td>Sequence is protein</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -slower1<br>-slower_sequence</td>
<td>boolean</td>
<td>Make lower case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -supper1<br>-supper_sequence</td>
<td>boolean</td>
<td>Make upper case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -scircular1<br>-scircular_sequence</td>
<td>boolean</td>
<td>Sequence is circular</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -squick1<br>-squick_sequence</td>
<td>boolean</td>
<td>Read id and sequence only</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sformat1<br>-sformat_sequence</td>
<td>string</td>
<td>Input sequence format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -iquery1<br>-iquery_sequence</td>
<td>string</td>
<td>Input query fields or ID list</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ioffset1<br>-ioffset_sequence</td>
<td>integer</td>
<td>Input start position offset</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sdbname1<br>-sdbname_sequence</td>
<td>string</td>
<td>Database name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sid1<br>-sid_sequence</td>
<td>string</td>
<td>Entryname</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ufo1<br>-ufo_sequence</td>
<td>string</td>
<td>UFO features</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fformat1<br>-fformat_sequence</td>
<td>string</td>
<td>Features format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fopenfile1<br>-fopenfile_sequence</td>
<td>string</td>
<td>Features file name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated outfile qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -odirectory2<br>-odirectory_outfile</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>


<H2>
    Input file format
</H2>

<b>prophecy</b> reads a protein or a nucleic sequence alignment USA.

<p>


<a name="input.1"></a>
<h3>Input files for usage example </h3>
<p><h3>File: globins.msf</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
!!AA_MULTIPLE_ALIGNMENT 1.0

  ../data/globins.msf MSF:  164 Type: P 25/06/01 CompCheck: 4278 ..

  Name: HBB_HUMAN Len: 164  Check: 6914 Weight: 0.61
  Name: HBB_HORSE Len: 164  Check: 6007 Weight: 0.65
  Name: HBA_HUMAN Len: 164  Check: 3921 Weight: 0.65
  Name: HBA_HORSE Len: 164  Check: 4770 Weight: 0.83
  Name: MYG_PHYCA Len: 164  Check: 7930 Weight: 1.00
  Name: GLB5_PETMA Len: 164  Check: 1857 Weight: 0.91
  Name: LGB2_LUPLU Len: 164  Check: 2879 Weight: 0.43

//

           1                                               50
HBB_HUMAN  ~~~~~~~~VHLTPEEKSAVTALWGKVN.VDEVGGEALGR.LLVVYPWTQR
HBB_HORSE  ~~~~~~~~VQLSGEEKAAVLALWDKVN.EEEVGGEALGR.LLVVYPWTQR
HBA_HUMAN  ~~~~~~~~~~~~~~VLSPADKTNVKAA.WGKVGAHAGEYGAEALERMFLS
HBA_HORSE  ~~~~~~~~~~~~~~VLSAADKTNVKAA.WSKVGGHAGEYGAEALERMFLG
MYG_PHYCA  ~~~~~~~VLSEGEWQLVLHVWAKVEAD.VAGHGQDILIR.LFKSHPETLE
GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE
LGB2_LUPLU ~~~~~~~~GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD

           51                                             100
HBB_HUMAN  FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE
HBB_HORSE  FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE
HBA_HUMAN  FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD
HBA_HORSE  FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD
MYG_PHYCA  KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ
GLB5_PETMA FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD
LGB2_LUPLU LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN

           101                                            150
HBB_HUMAN  LHCDKLH..VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA
HBB_HORSE  LHCDKLH..VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA
HBA_HUMAN  LHAHKLR..VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS
HBA_HORSE  LHAHKLR..VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS
MYG_PHYCA  SHATKHK..IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR
GLB5_PETMA LSGKHAK..SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA
LGB2_LUPLU LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA

           151        164
HBB_HUMAN  NALAHKYH~~~~~~
HBB_HORSE  NALAHKYH~~~~~~
HBA_HUMAN  TVLTSKYR~~~~~~
HBA_HORSE  TVLTSKYR~~~~~~
MYG_PHYCA  KDIAAKYKELGYQG
GLB5_PETMA Y~~~~~~~~~~~~~
LGB2_LUPLU IVIKKEMNDAA~~~

</pre>
</td></tr></table><p>


<H2>
    Output file format
</H2>

The output is a profile file.

<p>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: globins.prophecy</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
# Pure Frequency Matrix
# Columns are amino acid counts A-&gt;Z
# Rows are alignment positions 1-&gt;n
Simple
Name		globins
Length		164
Maximum score	496
Thresh		75
Consensus	PIVDTGSVVALSEEEKSAVDAAWVKANAVAEVGGHALERGLLALEPATLEFFDSFKDLSTFDASHGSAQVKAHGKKVLDALGAAVAHLDDLEGTLAALSDLHADKLHKGVDPVNFKLLSEALLVTLAAHFGADFTPEVQASLDKALAGVANVLAHKYHDAAYQG
0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  
0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  
0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  
0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  
0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  2  0  0  0  0  0  
1  0  0  0  0  0  1  0  0  0  0  1  0  0  0  0  0  0  0  0  0  2  0  0  0  0  0  
1  0  0  0  0  0  0  1  0  0  0  0  0  0  0  1  1  0  1  0  0  0  0  0  0  0  0  
0  0  0  0  1  0  0  0  0  0  0  4  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  2  2  0  0  0  0  0  0  0  
1  0  0  0  2  0  1  0  0  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  
1  0  0  0  2  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  1  0  0  0  0  
0  0  0  0  3  0  0  0  0  0  0  0  0  0  0  0  2  0  0  0  0  2  0  0  0  0  0  
1  0  0  0  0  0  0  0  0  0  3  3  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  
2  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  3  1  0  1  0  0  0  0  0  
3  0  0  0  0  0  0  0  0  0  1  2  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  
2  0  0  0  0  0  0  1  1  0  0  0  0  0  0  0  0  0  0  0  0  3  0  0  0  0  0  
0  0  0  2  0  0  0  0  0  0  1  1  0  0  0  0  0  1  0  1  0  1  0  0  0  0  0  
2  0  0  0  0  0  0  0  0  0  2  0  0  0  0  0  0  0  2  0  0  0  1  0  0  0  0  
2  0  0  0  0  0  0  0  0  0  0  2  0  0  0  0  0  0  1  2  0  0  0  0  0  0  0  
0  0  0  0  0  0  0  0  0  0  1  0  0  2  0  0  0  0  0  0  0  0  4  0  0  0  0  
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<font color=red>  [Part of this file has been deleted for brevity]</font>

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</pre>
</td></tr></table><p>

<a name="output.2"></a>
<h3>Output files for usage example 2</h3>
<p><h3>File: globins.prophecy</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
# Gribskov Protein Profile
# Columns are amino acids A-&gt;Z
# Last column is indel penalty
# Rows are alignment positions 1-&gt;n
Gribskov
Name		globins
Matrix		pprofile
Length		164
Max_score	939.76
Threshold	75
Gap_open	3.00
Gap_extend	0.30
Consensus	PIVDTGSVVSLSEEELSAVDKAWVKANSVAEVGGHALERGLFASEPMTLEFFDTFKYLSTFDLSKGSADVKAHGKKVLDALGDAVAHLDDLEGTLAALSDLHAHKLKKGVDPVNFKLLSHCLLVVLASHLPGDFTPEVQASMDKFLASVATVLASKYRELGYQG
0.65 0.00 0.13 0.13 0.13 -0.78 0.39 0.26 -0.26 0.00 0.13 -0.39 -0.26 0.00 0.00 1.95 0.39 0.39 0.52 0.39 0.00 0.13 -1.04 0.00 -1.04 0.00 0.87 0.87
0.00 0.00 0.26 -0.26 -0.26 0.78 -0.39 -0.39 1.95 0.00 -0.26 1.04 0.78 -0.39 0.00 -0.26 -0.39 -0.39 -0.13 0.26 0.00 1.43 -0.65 0.00 0.13 0.00 0.87 0.87
0.26 0.00 0.26 -0.26 -0.26 0.26 0.26 -0.39 1.43 0.00 -0.26 1.04 0.78 -0.39 0.00 0.13 -0.26 -0.39 -0.13 0.26 0.00 1.95 -1.04 0.00 -0.13 0.00 0.87 0.87
0.39 0.00 -0.65 1.95 1.30 -1.30 0.78 0.52 -0.26 0.00 0.39 -0.65 -0.52 0.78 0.00 0.13 0.78 0.00 0.26 0.26 0.00 -0.26 -1.43 0.00 -0.65 0.00 0.87 0.87
0.52 0.00 0.26 0.26 0.26 -0.39 0.52 -0.13 0.26 0.00 0.26 -0.13 0.00 0.26 0.00 0.39 -0.13 -0.13 0.39 1.95 0.00 0.26 -0.78 0.00 -0.39 0.00 0.87 0.87
0.78 0.00 0.26 0.78 0.65 -0.78 1.95 -0.26 -0.39 0.00 -0.13 -0.65 -0.39 0.52 0.00 0.39 0.26 -0.39 0.78 0.52 0.00 0.26 -1.30 0.00 -0.78 0.00 0.87 0.87
0.52 0.00 0.78 0.26 0.26 -0.39 0.78 -0.26 -0.13 0.00 0.26 -0.52 -0.39 0.39 0.00 0.52 -0.13 0.13 1.95 0.39 0.00 -0.13 0.39 0.00 -0.52 0.00 0.87 0.87
0.55 0.00 0.55 -0.55 -0.55 0.55 0.55 -0.82 3.00 0.00 -0.55 2.18 1.64 -0.82 0.00 0.27 -0.55 -0.82 -0.27 0.55 0.00 4.09 -2.18 0.00 -0.27 0.00 0.87 0.87
2.54 0.00 -0.27 -0.32 -0.09 1.06 1.35 -1.08 2.94 0.00 -0.85 3.15 2.61 -0.61 0.00 0.59 -0.12 -1.69 0.14 0.98 0.00 4.23 -2.38 0.00 -0.51 0.00 0.87 0.87
2.24 0.00 0.53 1.51 1.51 -2.35 1.63 1.78 -0.94 0.00 0.87 -1.29 -0.95 1.36 0.00 3.28 2.29 1.16 2.64 0.88 0.00 -0.34 -1.65 0.00 -2.09 0.00 0.87 0.87
0.06 0.00 -3.83 -0.43 1.03 3.60 -1.14 -0.17 2.69 0.00 -0.69 5.14 4.17 -0.77 0.00 -0.97 0.49 -1.49 -1.20 -0.09 0.00 2.69 0.29 0.00 0.40 0.00 0.87 0.87
2.34 0.00 1.92 1.60 1.46 -1.97 4.07 -0.88 -0.35 0.00 0.60 -1.75 -1.10 1.54 0.00 1.77 -0.09 -0.35 4.65 3.47 0.00 0.36 -1.65 0.00 -2.19 0.00 0.87 0.87
3.56 0.00 -0.56 3.08 4.01 -2.96 3.46 0.68 -0.86 0.00 0.61 -1.47 -0.86 1.65 0.00 2.44 1.93 -0.41 1.83 1.56 0.00 0.12 -4.91 0.00 -2.67 0.00 0.87 0.87
1.59 0.00 -2.04 0.74 1.64 -0.20 0.62 0.32 -1.14 0.00 0.81 -0.20 -0.97 0.92 0.00 -0.07 0.56 1.53 2.23 0.21 0.00 -1.30 -0.69 0.00 0.04 0.00 0.87 0.87
1.76 0.00 -2.66 3.90 5.45 -3.07 2.38 1.83 1.09 0.00 1.32 0.56 0.65 1.73 0.00 1.13 4.50 0.18 0.20 0.84 0.00 2.14 -6.12 0.00 -2.99 0.00 4.55 4.55
0.57 0.00 -4.51 -0.66 0.05 2.08 -1.71 -0.46 2.21 0.00 3.59 4.32 4.87 -0.05 0.00 -0.45 1.01 0.88 -0.55 0.51 0.00 2.34 1.59 0.00 -0.98 0.00 4.55 4.55
4.31 0.00 2.80 1.03 1.03 -1.77 3.52 -1.31 1.53 0.00 0.57 -0.34 -0.04 1.04 0.00 2.50 -0.41 -0.72 5.34 3.75 0.00 2.41 -2.26 0.00 -2.19 0.00 4.55 4.55
4.74 0.00 -1.43 0.36 0.77 -0.38 0.92 -0.39 1.19 0.00 1.43 2.10 2.53 0.30 0.00 2.40 1.19 -0.39 1.01 1.53 0.00 2.06 -1.98 0.00 -1.81 0.00 4.55 4.55
3.51 0.00 1.23 0.46 0.46 0.06 1.08 0.82 4.18 0.00 -0.60 2.47 1.80 0.02 0.00 1.32 0.41 -1.03 0.19 1.45 0.00 5.05 -4.42 0.00 -0.32 0.00 4.55 4.55
0.79 0.00 -2.10 2.78 1.91 -1.99 0.99 0.86 1.55 0.00 2.21 0.69 1.51 1.02 0.00 0.79 1.57 1.55 0.42 1.92 0.00 2.12 -1.78 0.00 -2.33 0.00 4.55 4.55
2.32 0.00 -1.29 -0.01 -0.01 -1.03 0.59 -0.49 -1.33 0.00 3.70 -0.87 -0.58 1.35 0.00 0.73 0.30 3.20 4.44 0.86 0.00 -1.40 1.49 0.00 -1.00 0.00 4.55 4.55
5.00 0.00 0.17 0.46 0.82 -0.02 1.95 -0.97 1.80 0.00 0.01 1.97 1.98 0.43 0.00 1.70 0.09 -1.69 1.93 4.27 0.00 2.35 -2.37 0.00 -1.16 0.00 4.55 4.55
-2.55 0.00 -5.95 -2.39 -2.60 2.54 -3.01 0.83 -2.78 0.00 3.36 0.58 -1.46 2.63 0.00 -2.83 -0.44 6.18 2.03 -1.52 0.00 -3.89 5.08 0.00 3.02 0.00 4.55 4.55
3.64 0.00 0.44 2.21 1.97 -1.76 3.66 -0.75 3.33 0.00 -0.33 1.62 1.37 0.41 0.00 1.42 0.65 -1.71 1.00 1.89 0.00 5.44 -6.44 0.00 -2.04 0.00 4.55 4.55
1.26 0.00 -3.44 3.35 4.37 -4.35 1.02 1.47 -1.45 0.00 6.61 -2.18 0.11 2.59 0.00 2.55 3.18 3.52 1.71 1.58 0.00 -1.06 -2.90 0.00 -4.41 0.00 4.55 4.55
5.63 0.00 1.62 -0.17 0.07 -0.23 2.38 -1.35 3.78 0.00 -0.99 2.86 2.17 -0.53 0.00 1.71 -0.40 -2.30 0.92 1.85 0.00 5.48 -4.58 0.00 -0.57 0.00 4.55 4.55
3.69 0.00 0.50 3.58 2.62 -2.00 2.31 1.96 -0.88 0.00 0.61 -1.50 -1.43 4.77 0.00 0.16 1.47 -1.17 1.34 1.22 0.00 -0.72 -2.56 0.00 0.36 0.00 4.55 4.55
1.44 0.00 0.96 0.44 0.44 -0.70 1.15 -0.32 -0.13 0.00 0.26 -0.58 -0.39 0.51 0.00 0.83 -0.01 -0.05 2.20 0.64 0.00 -0.01 -0.10 0.00 -0.70 0.00 3.49 3.49
-0.31 0.00 -2.56 -1.23 -0.83 1.74 -0.42 -0.35 1.36 0.00 0.54 2.24 0.38 0.32 0.00 -0.98 -0.84 1.99 1.16 1.45 0.00 1.65 -0.65 0.00 1.18 0.00 4.55 4.55
3.32 0.00 1.76 2.69 2.62 -1.00 2.98 0.36 0.29 0.00 -0.22 -0.91 -0.93 1.69 0.00 0.48 0.47 -1.55 2.69 1.39 0.00 0.54 -2.57 0.00 -0.35 0.00 4.55 4.55
2.09 0.00 -2.78 4.65 6.06 -4.35 3.67 1.29 -1.59 0.00 4.02 -2.46 -0.75 2.97 0.00 1.87 3.18 1.45 2.15 1.80 0.00 -0.70 -5.12 0.00 -4.17 0.00 4.55 4.55
1.16 0.00 0.53 0.23 0.23 -0.12 0.96 0.90 4.01 0.00 0.54 2.53 2.04 0.05 0.00 1.13 0.19 -0.10 -0.16 2.71 0.00 5.58 -3.99 0.00 -0.72 0.00 4.55 4.55
3.66 0.00 1.79 3.71 3.18 -3.66 8.67 -0.41 -1.92 0.00 -0.21 -3.31 -2.18 2.83 0.00 2.25 1.31 -1.17 5.03 2.47 0.00 0.75 -5.01 0.00 -3.54 0.00 4.55 4.55
4.50 0.00 0.40 3.83 3.40 -4.36 7.52 -0.15 -1.59 0.00 0.27 -2.44 -1.29 2.59 0.00 2.36 3.12 -1.05 2.98 2.86 0.00 0.88 -6.11 0.00 -3.89 0.00 4.55 4.55
0.96 0.00 -1.81 4.77 4.96 -2.52 1.47 4.99 -0.03 0.00 0.98 -0.76 -0.97 2.73 0.00 1.00 3.31 0.97 -0.03 0.63 0.00 0.49 -4.86 0.00 -0.93 0.00 4.55 4.55
6.08 0.00 0.63 2.84 2.19 -2.71 2.52 0.01 1.70 0.00 0.60 -0.14 0.46 1.20 0.00 1.99 1.38 -0.68 1.74 2.05 0.00 1.91 -4.48 0.00 -2.05 0.00 4.55 4.55
0.64 0.00 -1.96 -1.22 -0.54 4.31 0.80 -1.52 4.27 0.00 -1.81 5.56 4.33 -1.14 0.00 -0.96 -0.78 -2.62 -0.34 0.60 0.00 4.56 -0.41 0.00 0.63 0.00 4.55 4.55


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

0.68 0.00 -0.46 3.83 2.79 -1.46 1.37 3.83 -1.48 0.00 1.16 -1.91 -2.02 6.82 0.00 -0.89 1.86 -0.16 0.74 0.55 0.00 -1.76 -1.09 0.00 1.29 0.00 4.55 4.55
-1.76 0.00 -1.47 -5.11 -3.02 7.73 -3.04 -0.48 3.60 0.00 -3.02 7.19 3.72 -2.84 0.00 -1.20 -3.38 -2.45 -1.41 -1.11 0.00 2.18 5.11 0.00 5.28 0.00 4.55 4.55
0.46 0.00 -3.38 2.90 3.62 -4.43 0.41 2.59 -1.76 0.00 5.62 -2.10 0.37 2.26 0.00 2.21 4.56 5.10 1.00 0.58 0.00 -1.45 -0.16 0.00 -4.33 0.00 4.55 4.55
-1.37 0.00 -1.85 -4.16 -2.80 8.65 -3.47 -0.72 4.79 0.00 -2.93 8.47 5.65 -2.59 0.00 -3.01 -2.44 -3.24 -2.58 -1.09 0.00 4.21 4.61 0.00 4.92 0.00 4.55 4.55
-0.92 0.00 -2.85 -3.67 -2.36 7.63 -3.04 -1.53 6.73 0.00 -2.36 9.07 6.57 -2.83 0.00 -2.18 -1.98 -2.83 -2.16 -0.37 0.00 5.88 2.31 0.00 2.95 0.00 4.55 4.55
2.50 0.00 1.34 2.36 2.18 -3.29 4.63 -0.88 -1.28 0.00 3.40 -2.89 -1.22 2.55 0.00 2.15 0.77 1.35 6.78 2.17 0.00 -0.38 -0.55 0.00 -3.65 0.00 4.55 4.55
1.02 0.00 -1.72 3.71 4.55 -2.08 1.58 4.50 -0.15 0.00 1.28 -0.72 -0.80 4.39 0.00 0.76 2.95 0.85 0.40 0.82 0.00 0.37 -4.04 0.00 -0.70 0.00 4.55 4.55
3.93 0.00 3.10 -1.45 -1.41 0.69 1.36 -1.22 3.44 0.00 -2.02 1.49 1.37 -1.29 0.00 1.02 -1.35 -2.31 1.39 1.47 0.00 4.57 -4.96 0.00 1.71 0.00 4.55 4.55
1.56 0.00 -2.33 -1.98 -1.19 5.27 -1.79 -1.53 6.20 0.00 -1.58 7.38 5.92 -1.92 0.00 -0.93 -0.74 -2.57 -1.25 0.54 0.00 5.64 -0.10 0.00 0.99 0.00 4.55 4.55
2.04 0.00 -1.15 -1.62 -1.07 3.84 -0.65 -1.64 6.31 0.00 -1.46 6.55 5.21 -1.80 0.00 -0.27 -0.80 -2.45 -0.89 0.89 0.00 6.71 -1.83 0.00 0.39 0.00 4.55 4.55
1.22 0.00 2.14 -0.07 -0.16 -0.32 1.17 0.93 2.98 0.00 0.15 0.88 0.71 0.11 0.00 1.22 -0.17 0.12 1.82 1.14 0.00 4.24 -3.30 0.00 0.14 0.00 4.55 4.55
1.74 0.00 1.45 -0.36 -0.36 0.61 1.35 -1.63 6.05 0.00 -0.36 3.35 2.72 -0.81 0.00 0.88 -1.31 -1.63 0.37 5.00 0.00 6.82 -4.87 0.00 -1.01 0.00 4.55 4.55
1.42 0.00 -3.76 -2.40 -1.34 6.13 -2.08 -1.38 5.20 0.00 -1.73 8.38 6.78 -2.06 0.00 -1.08 -0.46 -2.71 -1.68 0.11 0.00 5.21 1.32 0.00 1.27 0.00 4.55 4.55
6.12 0.00 0.01 3.88 3.23 -3.77 2.78 2.33 -0.81 0.00 1.45 -1.51 -0.83 2.52 0.00 2.43 2.67 0.03 1.66 1.81 0.00 -0.03 -4.64 0.00 -1.76 0.00 4.55 4.55
2.54 0.00 0.90 1.55 1.86 -1.97 2.03 1.15 0.76 0.00 1.32 -0.58 0.08 1.35 0.00 2.06 0.94 1.21 2.83 2.93 0.00 1.42 -1.60 0.00 -1.96 0.00 4.55 4.55
-0.44 0.00 -0.44 1.18 1.18 -0.72 -0.83 6.01 0.50 0.00 1.15 0.18 0.26 1.53 0.00 1.40 2.54 3.53 -0.83 -0.15 0.00 1.27 -0.07 0.00 0.13 0.00 4.55 4.55
0.82 0.00 -1.50 -2.02 -0.88 4.57 -1.52 1.23 3.02 0.00 -1.69 5.41 3.38 -0.96 0.00 -0.72 -0.66 -1.61 -1.21 -0.25 0.00 2.80 1.54 0.00 2.95 0.00 4.55 4.55
5.17 0.00 1.23 2.19 1.95 -4.22 5.46 0.10 -1.43 0.00 0.11 -2.40 -1.43 1.23 0.00 6.69 1.81 -0.05 3.39 2.55 0.00 1.10 -6.29 0.00 -4.67 0.00 4.55 4.55
4.19 0.00 -0.43 3.35 2.96 -4.08 5.31 0.07 -1.53 0.00 2.90 -2.53 -0.81 3.90 0.00 1.77 2.05 0.28 2.97 2.31 0.00 0.14 -4.14 0.00 -3.30 0.00 4.55 4.55
1.99 0.00 -3.87 9.25 7.73 -6.29 3.74 2.72 -1.45 0.00 2.91 -3.15 -2.17 4.05 0.00 0.73 4.23 0.49 1.45 1.45 0.00 -1.45 -7.25 0.00 -3.69 0.00 4.55 4.55
-1.21 0.00 -0.88 -5.63 -3.49 8.10 -3.04 -0.73 2.90 0.00 -3.14 6.59 2.49 -2.60 0.00 -3.05 -4.32 -2.26 -0.90 -1.45 0.00 0.84 6.29 0.00 7.23 0.00 4.55 4.55
3.45 0.00 1.70 2.54 2.27 -3.00 6.03 -1.06 -0.10 0.00 0.63 -2.00 -1.00 2.06 0.00 2.24 0.09 -1.15 3.73 7.15 0.00 1.27 -4.89 0.00 -3.06 0.00 4.55 4.55
3.63 0.00 0.32 0.13 0.96 -1.48 1.56 0.76 -0.13 0.00 -0.20 0.06 -0.26 -0.06 0.00 5.87 0.79 0.10 1.87 1.48 0.00 0.81 -3.39 0.00 -2.18 0.00 4.55 4.55
4.89 0.00 -1.70 5.71 6.41 -4.71 3.81 1.67 -1.03 0.00 1.37 -2.04 -1.31 2.70 0.00 2.79 3.25 -0.37 2.05 1.96 0.00 -0.34 -7.09 0.00 -3.47 0.00 4.55 4.55
2.59 0.00 -0.99 -0.55 -0.24 0.95 0.55 -1.22 4.26 0.00 0.89 4.17 3.90 -0.71 0.00 0.68 0.05 -0.90 -0.08 1.27 0.00 5.74 -2.63 0.00 -1.04 0.00 4.55 4.55
0.43 0.00 -3.37 2.50 2.70 -1.54 -0.18 5.16 -0.75 0.00 1.36 0.96 0.74 2.75 0.00 1.00 6.23 1.89 -1.08 -0.54 0.00 -0.42 -1.36 0.00 -0.97 0.00 4.55 4.55
6.97 0.00 1.05 1.63 1.75 -2.35 4.47 -1.19 0.29 0.00 0.24 0.21 1.34 1.15 0.00 2.37 1.01 -1.28 2.95 2.32 0.00 1.79 -4.77 0.00 -2.41 0.00 4.55 4.55
6.11 0.00 3.48 1.74 1.74 -2.76 4.35 -1.16 -0.43 0.00 0.87 -2.03 -1.30 1.89 0.00 3.19 0.15 -0.44 7.68 2.47 0.00 0.15 -1.03 0.00 -2.61 0.00 4.55 4.55
-1.24 0.00 -2.27 -3.72 -2.76 6.98 -3.57 -0.76 3.20 0.00 -1.11 7.29 6.27 -2.03 0.00 -3.11 -1.60 -0.58 -2.20 -1.12 0.00 2.66 3.14 0.00 3.74 0.00 4.55 4.55
1.53 0.00 -2.18 4.97 3.77 -3.67 2.06 2.19 0.68 0.00 1.79 -0.83 -0.49 3.86 0.00 0.68 4.09 0.41 0.73 1.71 0.00 0.34 -4.67 0.00 -2.33 0.00 4.55 4.55
0.39 0.00 -1.13 0.83 0.70 -2.97 -0.46 0.22 0.11 0.00 7.11 -2.15 0.66 1.56 0.00 0.54 1.17 3.70 1.79 1.45 0.00 -0.13 -1.33 0.00 -1.84 0.00 4.55 4.55
2.37 0.00 1.02 -2.12 -1.28 3.29 -0.07 -1.35 5.20 0.00 -1.89 4.81 2.92 -1.58 0.00 -0.33 -2.03 -2.60 -0.13 0.80 0.00 4.96 -1.19 0.00 2.09 0.00 4.55 4.55
-0.31 0.00 -2.90 -3.09 -2.12 6.97 -2.43 -1.32 5.92 0.00 -2.18 8.89 6.83 -2.54 0.00 -1.76 -1.21 -2.85 -2.36 -0.31 0.00 6.51 1.66 0.00 2.19 0.00 4.55 4.55
5.05 0.00 -0.67 2.76 3.42 -1.63 2.78 0.05 0.51 0.00 0.46 0.47 0.67 1.46 0.00 1.65 1.52 -1.22 2.76 1.73 0.00 1.06 -3.42 0.00 -1.92 0.00 4.55 4.55
1.58 0.00 -0.27 1.40 1.82 -1.02 3.17 -0.17 -0.12 0.00 1.04 -0.31 0.68 1.22 0.00 1.41 0.89 1.05 3.93 1.20 0.00 0.78 0.56 0.00 -2.58 0.00 4.55 4.55
0.53 0.00 0.93 -2.26 -1.56 3.27 0.40 -1.70 5.52 0.00 -1.56 5.25 3.41 -1.74 0.00 -0.13 -2.12 -2.00 0.88 0.68 0.00 6.52 -0.72 0.00 1.13 0.00 4.55 4.55
5.99 0.00 1.95 1.54 1.54 -3.21 3.07 -0.08 -0.64 0.00 1.57 -1.79 -0.35 1.52 0.00 3.13 1.10 1.24 4.80 1.98 0.00 0.10 -0.48 0.00 -2.82 0.00 4.55 4.55
0.82 0.00 0.45 1.16 0.98 -0.33 0.46 1.04 0.65 0.00 2.38 -0.48 -0.02 3.38 0.00 -0.39 0.12 0.15 0.88 3.55 0.00 0.14 -0.54 0.00 0.34 0.00 4.55 4.55
3.67 0.00 0.37 2.14 1.42 -1.78 2.48 -0.43 2.72 0.00 -0.12 1.29 1.07 0.40 0.00 1.32 0.67 -1.36 0.73 1.55 0.00 4.17 -5.19 0.00 -1.53 0.00 0.92 0.92
-0.39 0.00 -2.72 -2.37 -1.58 5.92 -2.57 -1.40 6.20 0.00 -1.58 7.51 5.92 -2.18 0.00 -1.58 -1.00 -2.18 -1.77 0.02 0.00 5.38 0.94 0.00 1.38 0.00 0.92 0.92
5.69 0.00 1.02 1.58 1.58 -2.62 2.72 -0.47 0.30 0.00 1.34 -0.72 0.12 1.31 0.00 2.31 0.68 -0.69 2.05 4.59 0.00 0.95 -3.79 0.00 -1.97 0.00 0.92 0.92
2.81 0.00 1.15 1.76 1.76 -1.90 1.70 2.20 -0.87 0.00 1.52 -1.53 -1.05 2.07 0.00 1.98 1.40 1.17 3.51 1.15 0.00 -0.59 -0.63 0.00 -1.10 0.00 0.92 0.92
0.18 0.00 -3.57 2.22 2.52 -3.57 -0.23 0.78 -1.19 0.00 8.20 -1.79 0.95 2.44 0.00 0.60 2.51 4.27 1.19 1.19 0.00 -1.19 -0.14 0.00 -3.51 0.00 0.92 0.92
-1.60 0.00 4.97 -2.92 -2.79 7.25 -3.39 1.42 0.90 0.00 -3.08 2.34 0.39 -0.72 0.00 -4.40 -3.21 -3.08 -2.32 -1.60 0.00 -0.17 5.69 0.00 7.95 0.00 0.92 0.92
-0.69 0.00 -1.86 1.52 1.46 -2.40 -0.89 4.21 -1.64 0.00 4.26 -1.88 -0.02 2.60 0.00 1.14 2.74 5.28 0.32 0.02 0.00 -1.64 2.53 0.00 -1.65 0.00 0.92 0.92
0.61 0.00 -1.16 2.35 2.76 -1.47 1.08 0.82 -0.41 0.00 0.61 -0.74 -0.53 1.08 0.00 0.20 1.23 0.00 0.41 0.41 0.00 -0.41 -2.25 0.00 -1.02 0.00 0.92 0.92
0.78 0.00 -0.96 -0.53 -0.24 1.41 -0.35 -0.35 1.14 0.00 -0.43 2.08 1.71 -0.45 0.00 -0.12 -0.02 -0.76 -0.33 0.10 0.00 1.27 0.22 0.00 0.24 0.00 0.92 0.92
1.78 0.00 0.47 1.04 0.90 -1.16 2.51 -0.35 -0.43 0.00 -0.14 -0.78 -0.43 0.69 0.00 0.74 0.41 -0.61 1.10 0.82 0.00 0.41 -1.92 0.00 -1.04 0.00 0.92 0.92
-0.43 0.00 1.43 -0.71 -0.71 1.86 -0.86 0.43 0.14 0.00 -0.86 0.43 -0.14 -0.14 0.00 -1.14 -0.86 -0.86 -0.57 -0.43 0.00 -0.14 1.57 0.00 2.14 0.00 0.92 0.92
0.29 0.00 -0.86 0.86 0.86 -1.14 0.29 0.86 -0.43 0.00 0.57 -0.14 0.00 0.57 0.00 0.43 2.14 0.57 -0.14 -0.14 0.00 -0.29 -0.71 0.00 -0.86 0.00 0.92 0.92
0.86 0.00 0.29 0.86 0.71 -0.86 2.14 -0.29 -0.43 0.00 -0.14 -0.71 -0.43 0.57 0.00 0.43 0.29 -0.43 0.86 0.57 0.00 0.29 -1.43 0.00 -0.86 0.00 0.92 0.92
</pre>
</td></tr></table><p>

<p>

<h3>Simple frequency matrix</h3>

<p>

The columns represent amino acid counts for the amino acid residues from
A to Z.  The rows represent the alignment positions from 1->n.  The file
is a "Simple" frequency matrix of "Length" 20 amino acids.  The maximum
score this matrix can give is 496.  The "Threshold" value is an
instruction to the <b>profit</b> application to only report matches
above the given score. 

<p>

<h3>Gribskov profile</h3>

<p>

The columns represent the amino acids from A to Z, the rows denote the
alignment position from 1 to n.  The last column is the indel penalty. 
The "Name" is the name used by <b>prophet</b> to refer to the profile,
the "Matrix" is the name of the scoring matrix used (containing residue
substitution values).  "Length" is the length of the alignment. 
"Max_score" is the maximum score this profile can produce.  The
threshold is an instruction to <b>prophet</b> to only report hits equal
to or above the given value.  The gap opening and extension values are
used by <b>prophet</b> in the dynamic alignment (Smith Waterman
equivalent). 


<H2>
    Data files
</H2>


The two profile methods require a residue substitution scoring
matrix.

<p>

The Gribskov marices use the data file 'Epprofile' by default.  This is
derived from a PAM250 scoring matrix. 

<p>

The Henikoff matrices use the data file 'EBLOSUM62' by default.

<p>
EMBOSS data files are distributed with the application and stored
in the standard EMBOSS data directory, which is defined
by the EMBOSS environment variable EMBOSS_DATA.

<p>

To see the available EMBOSS data files, run:
<p>
<pre>
% embossdata -showall
</pre>
<p>
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:

<pre>

% embossdata -fetch -file Exxx.dat

</pre>
<p>

Users can provide their own data files in their own directories.
Project specific files can be put in the current directory, or for
tidier directory listings in a subdirectory called
".embossdata". Files for all EMBOSS runs can be put in the user's home
directory, or again in a subdirectory called ".embossdata".

<p>
The directories are searched in the following order:

<ul>
   <li> . (your current directory)
   <li> .embossdata (under your current directory)
   <li> ~/ (your home directory)
   <li> ~/.embossdata
</ul>
<p>

<H2>
    Notes
</H2>

<p>Profile analysis is a method for detecting distantly related proteins by sequence comparison. The basis for comparison is not only the customary Dayhoff mutational-distance matrix but also the results of structural studies and information implicit in the alignments of the sequences of families of similar proteins. This information is expressed in a position-specific scoring table (profile), which is created from a group of sequences previously aligned by structural or sequence similarity. The similarity of any other target sequence to the group of aligned probe sequences can be tested by comparing the target to the profile using dynamic programming algorithms. The profile method differs in two major respects from methods of sequence comparison in common use: (i) Any number of known sequences can be used to construct the profile, allowing more information to be used in the testing of the target than is possible with pairwise alignment methods. (ii) The profile includes the penalties for insertion or deletion at each position, which allow one to include the probe secondary structure in the testing scheme.</p>



<H2>
    References
</H2>

<ol>

<li> Gribskov M, McLachlan AD, Eisenberg D. Proc Natl Acad Sci U S
A. 1987 Jul; 84(13): 4355-8.

<li> Henikoff S, Henikoff JG. J Mol Biol. 1994 Nov 4; 243(4): 574-8.

</ol>

<H2>
    Warnings
</H2>

None.


<H2>
    Diagnostic Error Messages
</H2>

None.

<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="profit.html">profit</a></td>
<td>Scan one or more sequences with a simple frequency matrix</td>
</tr>

<tr>
<td><a href="prophet.html">prophet</a></td>
<td>Scan one or more sequences with a Gribskov or Henikoff profile</td>
</tr>

</table>

<H2>
    Author(s)
</H2>
Alan Bleasby 
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.


<H2>
    History
</H2>

1999 - Written Alan Bleasby.

<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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