[Genome] request

[Kate Rosenbloom]

Hello Andre,

Your best solution would be to download the full
set of multiz alignment files in .maf format from our downloads site:

http:hgdownload.cse.ucsc.edu/

and then to process the regions of interest to you locally.

Hope this helps,

	Kate
---
Kate Rosenbloom
UCSC Genome Bioinformatics

Andre Schuetzenmeister wrote:
> Hello,
> 
> my name is Andre Schuetzenmeister, I am a MSc student at the University
> of Leipzig, Germany. I use the UCSC-Genome Browser to recheck the
> conservation of binding sites which have previously classified conserved
> using PhastCons. I have already asked whether an R-interface exists to
> do this rechecking. I was told that no R-interface exists, thus, I
> decided to download all multiz-alignment pages and parse these
> HTML-pages to extract the alignments. 
> I had started my R-script, and after ~800 requests I got an error-page
> (see the text below) which told me to write to this email address in
> order to ask for more efficient ways to do my batch-job. 
> 
> Are there more efficient ways to obtain the multiz-alignments for
> hundreds or thousands of such genomic locations? This would speed up the
> computation a lot. 
> 
> I would be pleased to get an answer soon.
> 
> Sincerely, 
>    Andre Schuetzenmeister
> 
> 
> Your mesage :
> 
> There is a very high volume of traffic coming from your site (IP address
> 139.18.75.83) as of Mon Dec 11 07:12:45 2006 (California time). So that
> other users get a fair share of our bandwidth, we are putting in a delay
> of 12.9 seconds before we service your request. This delay will slowly
> decrease over a half hour as activity returns to normal. This high
> volume of traffic is likely due to program-driven rather than
> interactive access, or the submission of queries on a large number of
> sequences. If you are making large batch queries, please write to our
> genome at cse.ucsc.edu public mailing list and inquire about more efficient
> ways to access our data. If you are sharing an IP address with someone
> who is sumitting large batch queries, we apologize for the
> inconvenience. Please contact genome-www at cse.ucsc.edu if you think this
> delay is being imposed unfairly.
> 
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