User 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.

Submission by pasting the sequence:

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





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 value:
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: 		Properties: barthick
xbarpos ybarpos
Letters of first
assignment col: 		Properties: scale
xbarpos ybarpos
Bar of second
assignment col: 		Properties: barthick2
xbarpos2 ybarpos2
Letters of second
assignment col: 		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).
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 an mp file:

Read the mp file: (see the data format description)






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 value:
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: 		Properties: barthick
xbarpos ybarpos
Letters of first
assignment col: 		Properties: scale
xbarpos ybarpos
Bar of second
assignment col: 		Properties: barthick2
xbarpos2 ybarpos2
Letters of second
assignment col: 		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).
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):