| ## EMBOSS: cons

# Program cons

## Function

Creates a consensus from multiple alignments

## Description

cons 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.

The residue (or nucleotide) i in an alignment column, is compared to all other residues (j) in the column. The score for i is the sum over all residues j (not i=j) of the score(ij)*weight(j) . Where score(ij) is taken from a nucleotide or protein scoring matrix (see -datafile qualifier) and the "weight(j)" is the weighting given to the sequence j, which is given in the alignment file.

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 i are calculated as being the sum of weights of all the residues that increase the score of residue i (i.e. positive).

Where no consensus is found at a position i, an 'n' or an 'x' character is output; (depending on it being a DNA or protein sequence).

The "plurality" qualifier allows the user to set a cut-off for the number of positive matches below which there is no consensus.

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.

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.

## Usage

Here is a sample session with cons:

    % cons
    Creates a consensus from multiple alignments
    Input sequence set: aligned.fasta
    Output file [outfile.cons]: aligned.cons

## Command line arguments

       Mandatory qualifiers:
      [-msf]               seqset     File containing a sequence alignment.
      [-outseq]            seqout     Output sequence USA

       Optional qualifiers:
       -datafile           matrix     Scoring matrix
       -plurality          float      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.
       -identity           integer    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.
       -name               string     Name of the consensus sequence
       -setcase            float      Sets the threshold for the positive matches
                                      above which the consensus is is upper-case
                                      and below which the consensus is in
                                      lower-case.

       Advanced qualifiers: (none)
       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-msf] (Parameter 1) | File containing a sequence alignment. | Readable sequences | Required
[-outseq] (Parameter 2) | Output sequence USA | Writeable sequence | <sequence>.format
Optional qualifiers | Allowed values | Default
-datafile | Scoring matrix | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAFULL for DNA
-plurality | 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 integer value | Half the total sequence weighting
-identity | 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 | 0
-name | Name of the consensus sequence | Any string is accepted | An empty string is accepted
-setcase | 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 integer value | 0
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

The USA of a set of aligned sequences.

## Output file format

The output consists of a sequence file holding the consensus sequence. For example:

    >EMBOSS_001
    tagctgacctgacgggactgatgcgt

## Data files

It uses the standard set of scoring matrix data files.

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.

To see the available EMBOSS data files, run:

    % embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:

    % embossdata -fetch -file Exxx.dat

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".

The directories are searched in the following order:

- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
megamerger | Merge two large overlapping nucleic acid sequences
merger | Merge two overlapping nucleic acid sequences

## Author(s)

This application was written by Tim Carver (tcarver@hgmp.mrc.ac.uk)

## History

Written (Oct 2000) - Tim Carver

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments