reverse complementary logos

reverse complementary logos

Postby jvanheld » Wed Mar 10, 2010 1:37 pm

The program convert-matrix can (under other formats) export sequence logos, i.e. graphical representations of the information content and residue composition at each position of a position-specific scoring matrix (PSSM).

Logos are very convenient for visualizing and comparing motifs.

One frequent problem is that, since transcription factor binding sites are generally strand-insensitive, the orientation of a matrix is somewhat arbitrary. Thus, when comparing motifs, the similarities are not obvios if one motif is presented in one orientation and another motif in the other one.

To help visualizing the similarities between motifs, the program convert-matrix now exports two sequence logos for each matrix: one in direct orientation, and one in the reverse complementary orientation.
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