Welcome to the java-protein-domain-visualization wiki!

Project description

Project aims to develop a tool based on the Processing that helps in visualization of domain structure and repeats within proteins. Based on the idea of visualization of repeats in strings: Wattenberg, M. (2002) Arc Diagrams: Visualizing Structure in Strings. Proceedings of the IEEE Symposium on Information Visu-alization. IEEE Computer Society.
h1. Useful links

Here is original post on the visualization of the domain structure at Freelancing Science blog.

daTAA server has a first version implemented in its workflow.

Status of the first upload

Script has a number of things hardcoded, especially fonts and data file. Fonts need to go to the data subdirectory, while data itself are stored in the file (surprise, surprise) “data.txt” in the same directory as Processing script. Format of input data is as follows:

Length: 1259
O 99 1 23
H 20 161 175
H 17 360 405
CN 5 406 424
H 11 486 528
CN 5 529 547
H 11 605 638
CN 5 639 657
H 11 715 757
CN 5 758 776
CH 15 786 823
CN 5 824 845
CN 5 1104 1125
S 8 1133 1147
S 8 1156 1170
A 1 1171 125

Where the first line denotes length of the protein and following lines denote actual domains. Domain of the same type (H – heads, CN – N-connector, CH – H-connector, S – stalks) will be connected with arcs. Color code is simpler than that – you can encode various heads, connectors etc. and they will be colored according to master class (red, green, yellow), but connected with arcs only if they are of the same type.