Mutual information in protein sequences

Compute mutual information of your sequence alignment. You can submit the data by pasting the alignment, or read it from a file. When the processing is done you can zoom around in your plot as much as you want. For pure sequence information go to protein sequence logos. For publication of results, please cite

MatrixPlot: visualizing sequence constraints. J. Gorodkin, H. H. Stærfeldt, O. Lund, and S. Brunak. Bioinformatics. 15:769-770, 1999.

Submission by pasting the alignment:

Alignment: (see the data format description)

Mutual information options:

Zero's along the diagonal:

Complementary matrix elements (bp):

Alphabet:

Background nucleotide distribution (for logo profile):
A C D E F G H I K L M N P Q R S T V W Y - 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 1

MatrixPlot options:

Title: Title: size toffsetx toffsety

Color scale (interval R G B)
0.0 0.80 0.80 0.80 0.2 0.75 0.80 0.80 0.3 0.65 0.70 0.80 0.4 0.50 0.55 0.80 0.5 0.45 0.50 0.90 0.7 0.35 0.40 0.90 0.9 0.30 0.35 1.00 1.1 0.20 0.25 1.00 max 0.10 0.15 1.00

Color scale out:	Colorgrain:	Spacing:
Color: size xcoloff ycoloff
Grid: thickness xgridsize ygridsize

Show max mutual value:
Show sequence information profile:
Include gap profile (usegaps):
Reverse horizontal direction (xreverse):

Position numbers: size xnumpos ynumpos
Move baseline of info profile when having gaps in alignment:
Complementary matrix elements (cout):
Reverse vertical direction (yreverse):

Submission of a file containing the alignment: