CONSP

Creates a consensus from multiple alignments

cons calculates a consensus sequence from a multiple sequencealignment. To obtain the consensus, the sequence weights and a scoringmatrix are used to calculate a score at each position in the alignment.

The residue (or nucleotide) i in an alignment column, is comparedto all other residues (j) in the column. The score for iis the sum over all residues j (not i=j) of thescore(ij)*weight(j) . Where score(ij) is takenfrom a nucleotide or protein scoring matrix (see -datafilequalifier) and the "weight(j)" is the weighting given to thesequence j, which is given in the alignment file.

The highest scoring type of residue is then found in the column. If thenumber of positive matches for this residue is greater than the"plurality value" then this residue is the consensus. The positivematches for a residue i are calculated as being the sum ofweights 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 thenumber of positive matches below which there is no consensus.

The "identity" qualifier provides the facility of setting the requirednumber of identities at a site for it to give a consensus at thatposition. Therefore, if this is set to the number of sequences in thealignment only columns of identities contribute to the consensus.

The "setcase" qualifier sets the threshold for the positive matchesabove which the consensus is is upper-case and below which the consensusis in lower-case.