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<HTML>
<HEAD>
<TITLE>
EMBOSS: profit
</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">
profit
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Scan a sequence or database with a matrix or profile
<H2>
Description
</H2>
<b>profit</b> takes a simple frequency matrix produced by
<b>prophecy</b> and searches with this to find matches in the input
sequence(s) you are searching.
<p>
Scores for the matches are calculated from the simple frequency matrix.
It is the sum of scores at each position of the matrix.
<p>
A 'simple frequency matrix' is simply a count of the number of times any
particular amino acid occurs at each position in the alignment used to
create it. Simple frequency matrices are created using the program
<b>prophecy</b> with the option '-type F' to create the correct type of
matrix. The alignment should not have gaps in it.
<p>
The resulting matrix is moved to each position in the sequence(s) you
are searching. At each position in the sequence, the frequencies of the
amino acids or bases covered by the length of the matrix is read from
the matrix. The sum of these frequencies at each position of the matrix
is the score for that position of the sequence. If this score is above
the threshold percentage of the maximum possible score for that matrix,
then a hit is reported.
<H2>
Usage
</H2>
Before running the example, we need to make a simple frequency matrix
using <b>prophecy</b>
<p>
This is the ungapped aligned set of sequences used to make the matrix:
<p>
<pre>
% more m.seq
>one
DEVGGEALGRLLVVYPWTQR
>two
DEVGREALGRLLVVYPWTQR
>three
DEVGGEALGRILVVYPWTQR
>four
DEVGGEAAGRVLVVYPWTQR
<p>
% prophecy
Creates matrices/profiles from multiple alignments
Input sequence set: m.seq
Profile type
F : Frequency
G : Gribskov
H : Henikoff
Select type [F]:
Enter a name for the profile [mymatrix]:
Enter threshold reporting percentage [75]:
Output file [outfile.prophecy]:
</pre>
<p>
<b>Here is a sample session with profit</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>profit </b>
Scan a sequence or database with a matrix or profile
Profile or weight matrix file: <b>outfile.prophecy</b>
Input sequence(s): <b>tsw:*</b>
Output file [outfile.profit]: <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:
[-infile] infile Profile or weight matrix file
[-sequence] seqall Sequence(s) filename and optional format, or
reference (input USA)
[-outfile] outfile [*.profit] Output file name
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin2 integer Start of each sequence to be used
-send2 integer End of each sequence to be used
-sreverse2 boolean Reverse (if DNA)
-sask2 boolean Ask for begin/end/reverse
-snucleotide2 boolean Sequence is nucleotide
-sprotein2 boolean Sequence is protein
-slower2 boolean Make lower case
-supper2 boolean Make upper case
-sformat2 string Input sequence format
-sdbname2 string Database name
-sid2 string Entryname
-ufo2 string UFO features
-fformat2 string Features format
-fopenfile2 string Features file name
"-outfile" associated qualifiers
-odirectory3 string Output directory
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>[-infile]<br>(Parameter 1)</td>
<td>Profile or weight matrix file</td>
<td>Input file</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>[-sequence]<br>(Parameter 2)</td>
<td>Sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 3)</td>
<td>Output file name</td>
<td>Output file</td>
<td><i><*></i>.profit</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 colspan=4>(none)</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>profit</b> reads a simple frequency matrix produced by
<b>prophecy</b> and uses it to search searches one or more protein or
nucleic acid sequence USAs.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tsw:*' is a sequence entry in the example protein database 'tsw'
<p>
<p><h3>File: outfile.prophecy</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
# Pure Frequency Matrix
# Columns are amino acid counts A->Z
# Rows are alignment positions 1->n
Simple
Name mymatrix
Length 20
Maximum score 76
Thresh 75
Consensus DEVGGEALGRLLVVYPWTQR
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 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 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0
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 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 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 0
4 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 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 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 0 1 0 0 0 0 0
0 0 0 0 0 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 0 0 0 0 0 0 0 0 0 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 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 0 0 0 0 0 0 0 0 4 0 0
0 0 0 0 0 0 0 0 0 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 0 0 0 0 0 0 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 0 0 4 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 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 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: outfile.profit</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
# PROF scan using simple frequency matrix mymatrix
# Scores >= threshold 75 (max score 76)
#
HBB_HUMAN 22 Percentage: 100
HBB_PANPA 22 Percentage: 100
HBB_PANTR 22 Percentage: 100
</pre>
</td></tr></table><p>
<p>
The ouput is a list of three columns.
<p>
The first column is the name of the matching sequence found.
<br>
The second is the start position in the sequence of the match.
<br>
The third column (after the word 'Percentage:') is the percentage of the
maximum possible score (sum of the highest value at each
position in the frequency matrix).
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
None.
<H2>
References
</H2>
None.
<H2>
Warnings
</H2>
The aligned set of sequences used to make the simple frquency matrix
should not have gaps in it. <b>profit</b> will let you use a matrix
made from a gapped alignment, but the results will probably not be
sensible.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It always exits with a status of 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="prophecy.html">prophecy</a></td>
<td>Creates matrices/profiles from multiple alignments</td>
</tr>
<tr>
<td><a href="prophet.html">prophet</a></td>
<td>Gapped alignment for profiles</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Alan Bleasby (ajb © ebi.ac.uk)
<br>
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
Written (1999) - 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
</BODY>
</HTML>
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