An Introduction to Profiles
by Roderic Guigo, IMIM and UB, Barcelona
bugs. It has been only tested on Netscape clients---version 3 and higher---
running on Silicon Graphics.
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
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.
But usually you are only interested in the scores over a given threshold.
Often, you set such a threshold at the minimum value scored by the sequences
from which the profile has been derived. For instance, the minimum
value scored by the original sequences from which above profile has been
Of course, you can play with the threshold and increase or decrease the number
of potential matches, incresing and decreasing accordingly sensitivity and
specificity (Change the value of the threshold and click on "ScanSequence"