Intelligent Systems Laboratory
wm_match and wm_align
wm_match
Transcription factor (TF) binding sites are often represented as weight matrices, for example in the TransFac database. Still it may be a complicated task to find the sequences that match a given weight matrix. The idea behind the wm_match approach is to use weight matrix entropies as a measure of a match.
wm_align
The wm_align program aligns short DNA sequences (up to 50 bp), and gives a weight matrix as output. The algorithm computes entropies to find the best way of arranging the sequences into a weight matrix. One application of the program is to create a TF weight matrix from a set of TF binding site observations.