[Genome] question about custom tracks

[Ge Zhang]

Dear Sir or Madam,

First I would like to appreciate your efforts in creating and maintaining
this excellent free resource for bioscientist. The custom track utility
provides tremendous help to our research. I have several question about how
to use it:

1. How to create a item with different colors? For example, if I want to
create a item (GFF group) to show a block with several SNP markers, the
ideal way is to use a rectangle (in light gray) for the whole block and
several vertical lines (in black, or in different colors showing their
functional significance) for each SNP. I try to use GFF format to describe
such feature in the following way, but it seems to me that the Genome
Browser will only display each feature with the color for the HIGHEST score
(in our case, 1000 for each SNP marker).

browser position chr1:213742472-213941141
browser hide all
track name=Block description="SNP Blocks" visibility=1 color=0,128,0
useScore=1
chr1    BlockFinder    Block    213753472    213759167    400    .    .
Block_1
chr1    BlockFinder    SNP    213743472    213743472    1000    .    .
Block_1
chr1    BlockFinder    SNP    213747205    213747206    1000    .    .
Block_1
chr1    BlockFinder    SNP    213749167    213749168    1000    .    .
Block_1
chr1    BlockFinder    Block    213762463    213780713    400    .    .
Block_2
chr1    BlockFinder    SNP    213762463    213762464    1000    .    .
Block_2
chr1    BlockFinder    SNP    213764076    213764077    1000    .    .
Block_2
chr1    BlockFinder    SNP    213769724    213769725    1000    .    .
Block_2
chr1    BlockFinder    SNP    213780713    213780714    1000    .    .
Block_2

2. Is there any way to override the maximum image width limitation (5000
pixels), because in order to display some fine features for a long genomic
region 5000 pixels is not enough.

3. How to create a custom track showing pairwise relationship among genomic
elements? For example the pairwise LD similar to the HapMap LD track
included in the hg17 database (
http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=hapmapLd).

4. In order to lower the computational loads of your site, we are thinking
to build a stand along application using the power of Genome Browser in
generating high quality graphic representation for genomic annotations.
Therefore, the question is: can we use the specific codes for drawing custom
tracks from Genome Browser and build a light-weight application instead of
mirror the whole Genome Browser on our sever. If it is possible, what is the
license requirement (for academic use only) and how to locate those codes?

Thank you for your help!

Best regards,

Ge Zhang
Center for Genome Information
University of Cincinnati Medical Center