A Profile or Position Weigth Matrix (the two terms are used synonymously here) is a motif descriptor. It attempts to capture the intrinsic variability characteristic of sequence patterns. A Profile it is usually derived from a set of aligned sequences functionally related. For instance, below we have the sequence of ten vertebrate donor sites, aligned at the boundary exon/intron.
As a result of scaning the sequence with the matrix, you obtain an score at each position. Click on 'ScanSequence' for the whole list of scores along the sequence.Roderic Guigo (i Serra), IMIM and UB. email@example.com