cons

Function

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

Command line arguments


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.

Data files

It uses the standard set of scoring matrix data files.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Author(s)

History

Target users

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