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<HTML>
<HEAD>
<TITLE>
EMBOSS: cons
</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">
cons
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Creates a consensus from multiple alignments
<H2>
Description
</H2>
<b>cons</b> calculates a consensus sequence from a multiple sequence
alignment. To obtain the consensus, the sequence weights and a scoring
matrix are used to calculate a score at each position in the alignment.
<P>
The residue (or nucleotide) <b>i</b> in an alignment column, is compared
to all other residues (<b>j</b>) in the column. The score for <b>i</b>
is the sum over all residues <b>j</b> (not <b>i=j</b>) of the
score(<b>ij</b>)*weight(<b>j</b>) . Where score(<b>ij</b>) is taken
from a nucleotide or protein scoring matrix (see <b>-datafile</b>
qualifier) and the "weight(<b>j</b>)" is the weighting given to the
sequence <b>j</b>, which is given in the alignment file.
<P>
The highest scoring type of residue is then found in the column. If the
number of positive matches for this residue is greater than the
"plurality value" then this residue is the consensus. The positive
matches for a residue <b>i</b> are calculated as being the sum of
weights of all the residues that increase the score of residue <b>i</b>
(i.e. positive).
<P>
Where no consensus is found at a position <b>i</b>, an 'n' or an 'x'
character is output; (depending on it being a DNA or protein sequence).
<P>
The "plurality" qualifier allows the user to set a cut-off for the
number of positive matches below which there is no consensus.
<P>
The "identity" qualifier provides the facility of setting the required
number of identities at a site for it to give a consensus at that
position. Therefore, if this is set to the number of sequences in the
alignment only columns of identities contribute to the consensus.
<P>
The "setcase" qualifier sets the threshold for the positive matches
above which the consensus is is upper-case and below which the consensus
is in lower-case.
<P>
<H2>
Usage
</H2>
<b>Here is a sample session with cons</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>cons </b>
Creates a consensus from multiple alignments
Input (aligned) sequence set: <b>dna.msf</b>
output sequence [dna.fasta]: <b>aligned.cons</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] seqset File containing a sequence alignment.
[-outseq] seqout [<sequence>.<format>] Sequence filename and
optional format (output USA)
Additional (Optional) qualifiers:
-datafile matrix [EBLOSUM62 for protein, EDNAFULL for DNA]
This is the scoring matrix file used when
comparing sequences. By default it is the
file 'EBLOSUM62' (for proteins) or the file
'EDNAFULL' (for nucleic sequences). These
files are found in the 'data' directory of
the EMBOSS installation.
-plurality float [Half the total sequence weighting] Set a
cut-off for the number of positive matches
below which there is no consensus. The
default plurality is taken as half the total
weight of all the sequences in the
alignment. (Any numeric value)
-identity integer [0] Provides the facility of setting the
required number of identities at a site for
it to give a consensus at that position.
Therefore, if this is set to the number of
sequences in the alignment only columns of
identities contribute to the consensus.
(Integer 0 or more)
-setcase float [@( $(sequence.totweight) / 2)] Sets the
threshold for the positive matches above
which the consensus is is upper-case and
below which the consensus is in lower-case.
(Any numeric value)
-name string Name of the consensus sequence (Any string
is accepted)
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
"-outseq" associated qualifiers
-osformat2 string Output seq format
-osextension2 string File name extension
-osname2 string Base file name
-osdirectory2 string Output directory
-osdbname2 string Database name to add
-ossingle2 boolean Separate file for each entry
-oufo2 string UFO features
-offormat2 string Features format
-ofname2 string Features file name
-ofdirectory2 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>[-sequence]<br>(Parameter 1)</td>
<td>File containing a sequence alignment.</td>
<td>Readable set of sequences</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>[-outseq]<br>(Parameter 2)</td>
<td>Sequence filename and optional format (output USA)</td>
<td>Writeable sequence</td>
<td><i><*></i>.<i>format</i></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>-datafile</td>
<td>This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation.</td>
<td>Comparison matrix file in EMBOSS data path</td>
<td>EBLOSUM62 for protein<br>EDNAFULL for DNA</td>
</tr>
<tr>
<td>-plurality</td>
<td>Set a cut-off for the number of positive matches below which there is no consensus. The default plurality is taken as half the total weight of all the sequences in the alignment.</td>
<td>Any numeric value</td>
<td>Half the total sequence weighting</td>
</tr>
<tr>
<td>-identity</td>
<td>Provides the facility of setting the required number of identities at a site for it to give a consensus at that position. Therefore, if this is set to the number of sequences in the alignment only columns of identities contribute to the consensus.</td>
<td>Integer 0 or more</td>
<td>0</td>
</tr>
<tr>
<td>-setcase</td>
<td>Sets the threshold for the positive matches above which the consensus is is upper-case and below which the consensus is in lower-case.</td>
<td>Any numeric value</td>
<td>@( $(sequence.totweight) / 2)</td>
</tr>
<tr>
<td>-name</td>
<td>Name of the consensus sequence</td>
<td>Any string is accepted</td>
<td><i>An empty string is accepted</i></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>
The USA of a set of aligned sequences.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
<p><h3>File: dna.msf</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
!!NA_MULTIPLE_ALIGNMENT
dna.msf MSF: 120 Type: N January 01, 1776 12:00 Check: 3196 ..
Name: MSFM1 Len: 120 Check: 8587 Weight: 1.00
Name: MSFM2 Len: 120 Check: 6178 Weight: 1.00
Name: MSFM3 Len: 120 Check: 8431 Weight: 1.00
//
MSFM1 ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC
MSFM2 ACGTACGTAC GTACGTACGT ....ACGTAC GTACGTACGT ACGTACGTAC
MSFM3 ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT CGTACGTACG
MSFM1 GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT
MSFM2 GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT
MSFM3 TACGTACGTA CGTACGTACG TACGTACGTA ACGTACGTAC GTACGTACGT
MSFM1 ACGTACGTAC GTACGTACGT
MSFM2 ACGTACGTTG CAACGTACGT
MSFM3 ACGTACGTAC GTACGTACGT
</pre>
</td></tr></table><p>
<H2>
Output file format
</H2>
The output consists of a sequence file holding the consensus sequence.
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: aligned.cons</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
>EMBOSS_001
ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
It uses the standard set of scoring matrix data files.
<P>
<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>
None.
<H2>
References
</H2>
None.
<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="megamerger.html">megamerger</a></td>
<td>Merge two large overlapping nucleic acid sequences</td>
</tr>
<tr>
<td><a href="merger.html">merger</a></td>
<td>Merge two overlapping sequences</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Tim Carver (tcarver © rfcgr.mrc.ac.uk)
<br>
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
<H2>
History
</H2>
<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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