Distance matrices

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.

Submission by pasting the sequence:

Give PDB entry (small letters) (and chain, capital letter):
OR
Type in the sequence with 3D coordinates: (see the 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)
4 1.00 0.00 0.00 10 1.00 0.40 0.00 20 1.00 0.90 0.00 30 0.60 0.90 0.10 40 0.20 0.70 0.10 50 0.00 0.30 0.10 60 0.00 0.45 0.50 70 0.00 0.20 0.60 85 0.00 0.00 0.40

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 (small letters) (and chain, capital letter):
OR
Read the sequence file with 3D coordinates: (see the 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)
4 1.00 0.00 0.00 10 1.00 0.40 0.00 20 1.00 0.90 0.00 30 0.60 0.90 0.10 40 0.20 0.70 0.10 50 0.00 0.30 0.10 60 0.00 0.45 0.50 70 0.00 0.20 0.60 85 0.00 0.00 0.40

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):