Events News Research CBS CBS Publications Bioinformatics
Staff Contact About Internal CBS CBS Other

MatrixPlot 1.2: Mutual information in protein sequences

Introduction Data format User matrix Mutual Nucl Mutual Prot Dist matrix

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. (http://www.cbs.dtu.dk/services/MatrixPlot/)

*

Submission by pasting the alignment:

Alignment: (data format description)


*

Mutual information options:
Zero's along the diagonal:
Complementary matrix elements (bp):
Alphabet:
Background nucleotide distribution
(for logo profile):
*

MatrixPlot options:
Title:
Title: size toffsetx toffsety
Color scale (interval R G B)
Color scale out:
Colorgrain:
Spacing:
Color: size
xcoloff ycoloff

Grid: thickness
xgridsize ygridsize
Show max
mutual value:
Position numbers:
size xnumpos ynumpos
Show sequence
information profile:
Move baseline of info profile
when having gaps in alignment:
Include gap
profile (usegaps):
Complementary matrix
elements (cout):
Reverse horizontal
direction (xreverse):
Reverse vertical
direction (yreverse):
*

Submission of a file containing the alignment:

Alignment: (data format description)


*

Mutual information options:
Zero's along the diagonal:
Complementary matrix elements (bp):
Alphabet:
Background nucleotide distribution
(for logo profile):
*

MatrixPlot options:
Title:
Title: size toffsetx toffsety
Color scale (interval R G B)
Color scale out:
Colorgrain:
Spacing:
Color: size
xcoloff ycoloff

Grid: thickness
xgridsize ygridsize
Show max
mutual value:
Position numbers:
size xnumpos ynumpos
Show sequence
information profile:
Move baseline of info profile
when having gaps in alignment:
Include gap
profile (usegaps):
Complementary matrix
elements (cout):
Reverse horizontal
direction (xreverse):
Reverse vertical
direction (yreverse):



GETTING HELP

Scientific problems:        Technical problems: