MatrixPlot 1.2: User Matrix

Introduction

Data format

User matrix

Mutual Nucl

Mutual Prot

Dist matrix

Submit your own computed matrix plot file by pasting it in, or read it from a file. 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 sequence:

Type in the sequence with 3D coordinates: (data format description)



MatrixPlot options:

Title:

Title: size toffsetx toffsety

Color scale (interval R G B)

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

Show max value:	Yes No	Position numbers: size xnumpos ynumpos

Assignment along the edges of the matrix plot. Note that the "Letter" option overwrite the "Bar" option for each of the two possible assignments.
Bar of first assignment col:	No Yes	Properties: barthick xbarpos ybarpos
Letters of first assignment col:	No Yes	Properties: scale xbarpos ybarpos
Bar of second assignment col:	No Yes	Properties: barthick2 xbarpos2 ybarpos2
Letters of second assignment col:	No Yes	Properties: scale xbarpos2 ybarpos2

The bars and letters can be replaced by one entire text string. Read all cols as one string (you can have more than two cols).

No Yes

Show sequence information profile:	No Yes	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 an mp file:

Read the mp file: (data format description)



MatrixPlot options:

Title:

Title: size toffsetx toffsety

Color scale (interval R G B)

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

Show max value:	Yes No	Position numbers: size xnumpos ynumpos

Assignment along the edges of the matrix plot. Note that the "Letter" option overwrite the "Bar" option for each of the two possible assignments.
Bar of first assignment col:	No Yes	Properties: barthick xbarpos ybarpos
Letters of first assignment col:	No Yes	Properties: scale xbarpos ybarpos
Bar of second assignment col:	No Yes	Properties: barthick2 xbarpos2 ybarpos2
Letters of second assignment col:	No Yes	Properties: scale xbarpos2 ybarpos2

The bars and letters can be replaced by one entire text string. Read all cols as one string (you can have more than two cols).

No Yes

Show sequence information profile:	No Yes	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

---

GETTING HELP

Scientific problems:        Technical problems:       

---