[Genome] BLAT Search Genome: hgc XML output?

[John Woods]

I've Googled quite a bit for this, but no luck. I also see that 
BioPython has a BLAT parser which will output XML, which leads me to 
believe that the answer to my question will be no. But I thought I 
should ask anyway--before reinventing the wheel.

So, the BLAT Search Rsults outputs this nice list with links to browser 
and details. If I click on "details" for a hit, I get cgi-bin/hgc, which 
highlights--in both the query and the match--the portions of the 
sequence which align well.

Is it possible to get XML output for this page? Particularly, I'd like 
to be able to extract both the aligned an unaligned portions of sequence 
(from both query and result) in some sort of array or list.

Alternatively, is there pal2nal functionality for this script?

And finally, if the answer to both of those is no, any recommendations 
for parsers? I can't find the docs on BioPython's BLAT parser, sadly.

Thanks very much!

Cheers,
John Woods

Institute for Cellular and Molecular Biology
The University of Texas at Austin