Mutual information in RNA and DNA 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 sequence-structure 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:

Compute by
Zero's along the diagonal:
Complementary matrix elements (bp):
Alphabet:
Background nucleotide distribution (for logo profile):	`A C G UT - 0.25 0.25 0.25 0.25 1`
Complementarity matrix (when using type 2)	`A C G UT - A 0 0 0 1 0 C 0 0 1 0 0 G 0 1 0 1 0 UT 1 0 1 0 0 - 0 0 0 0 0`

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:

Alignment: (see the data format description)

Mutual information options:

Compute by
Zero's along the diagonal:
Complementary matrix elements (bp):
Alphabet:
Background nucleotide distribution (for logo profile):	`A C G UT - 0.25 0.25 0.25 0.25 1`
Complementarity matrix (when using type 2)	`A C G UT - A 0 0 0 1 0 C 0 0 1 0 0 G 0 1 0 1 0 UT 1 0 1 0 0 - 0 0 0 0 0`

MatrixPlot options:

Title: Title: size toffsetx toffsety

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):