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MatrixPlot 1.2: Distance matrices

Introduction Data format User matrix Mutual Nucl Mutual Prot Dist matrix

Get a distance matrix of an RNA or DNA sequence with 3D coordinates. You can submit the sequence with its 3D coordinates by pasting it in, or read it from a file. You can also type a PDB entry name with corresponding chain identifier. After return of the matrix plot you can zoom around in it. 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:

Give PDB entry (and chain):
OR
Type in the sequence with 3D coordinates: (data format description)


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pdb2mp column format options: (Ignore if you are using PDB format)
xcol:
ycol:
zcol:
acol:
scol:
*

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
distance:
Position numbers:
size xnumpos ynumpos
Secondary
structure bar
Structure bar:
barthick xbarpos ybarpos
Sequence
letters
Sequence letters:
scale xbarpos2 ybarpos2
Complementary matrix
elements (cout):
Reverse horizontal
direction (xreverse):
Reverse vertical
direction (yreverse):
*

Submission of a file containing the sequence:

Give PDB entry (and chain):
OR
Read the sequence file with 3D coordinates: (data format description)


*

pdb2mp column format options: (Ignore if you are using PDB format)
xcol:
ycol:
zcol:
acol:
scol:
*

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
distance:
Position numbers:
size xnumpos ynumpos
Secondary
structure bar
Structure bar:
barthick xbarpos ybarpos
Sequence
letters
Sequence letters:
scale xbarpos2 ybarpos2
Complementary matrix
elements (cout):
Reverse horizontal
direction (xreverse):
Reverse vertical
direction (yreverse):



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