MatrixPlot 1.2: Mutual information in RNA and DNA 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 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. (http://www.cbs.dtu.dk/services/MatrixPlot/)

Submission by pasting the alignment:

Alignment: (data format description)



Mutual information options:

Compute by mtype=2 mtype=1

Zero's along the diagonal: No Yes

Complementary matrix elements (bp): No Yes

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: Yes No Colorgrain: No Yes Spacing: Color: size xcoloff ycoloff Grid: thickness xgridsize ygridsize

Show max mutual value:	Yes No	Position numbers: size xnumpos ynumpos
Show sequence information profile:	Yes No	Move baseline of info profile when having gaps in alignment:	No Yes
Include gap profile (usegaps):	Yes No	Complementary matrix elements (cout):	No Yes
Reverse horizontal direction (xreverse):	No Yes	Reverse vertical direction (yreverse):	No Yes

Submission of a file containing the alignment:

Alignment: (data format description)



Mutual information options:

Compute by mtype=2 mtype=1

Zero's along the diagonal: No Yes

Complementary matrix elements (bp): No Yes

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: Yes No Colorgrain: No Yes Spacing: Color: size xcoloff ycoloff Grid: thickness xgridsize ygridsize

Show max mutual value:	Yes No	Position numbers: size xnumpos ynumpos
Show sequence information profile:	Yes No	Move baseline of info profile when having gaps in alignment:	No Yes
Include gap profile (usegaps):	Yes No	Complementary matrix elements (cout):	No Yes
Reverse horizontal direction (xreverse):	No Yes	Reverse vertical direction (yreverse):	No Yes

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GETTING HELP

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