Mapwhere

MAPWHERE is a program that finds perfect or partial matches to motifs in (protein) sequences.

MAPWHERE's motifs are defined by position-specific scores and by the maximum and minimum distances allowed between these modelled positions. If the user is interested in partial matches, he has to provide a cutoff value.

MAPWHERE is designed for motifs with a few well-conserved positions in an otherwise non-conserved environment or for short blocks with almost perfect conservation. The motifs extend PROSITE patterns in that the positions can be weighted, differentially scored, and partial matches, defined by a cutoff score, are reported as well.

There are no penalties for mismatches nor for gaps. As the distances between the conserved positions might vary considerably they are considered uninformative. At the single positions every residue can be given a different integer score, in principle like in a PSSM. Therefore, the motifs extend PSSMs by allowing for gaps between the positions, but gaps are not scored like they would in profiles.

The algorithm performs extensive search and is guaranteed to others with a higher score are reported. By default every match is scored 1 point and the cut-off is equal to the number of positions in the expression that is perfect matches.

The various positions in the expression can be weighted, currently scores from 1 to 999 are accepted; the weights can be different for different residues at the same position. Distances can be between 0 and 999. The input consists in one or more expressions in MAPWHERE syntax (explained below, easy to use) and one or more protein sequences in fasta format.

The algorithm is based on recursions that keep trace of the matches and adapt the allowed distances as needed when searching for partial matches. It runs quite fast as long as the expressions are not too complicate. A slow down can be oserved when considerable variation in the distances are allowed and when the cutoff lies strongly below the maximum score.

It was tested under UNIX and LINUX and can be compiled using the included makefile that calls the gcc compiler. A README file with Instructions for Installation and Usage can be found here