Instead of hitting the site more than 1000 times (or more, will this analysis be repeated?), have you considered doing the scoring on your end? The link you provided contains a link that describes how the scores are calculated (http://thr.cit.nih.gov/molbio/hla_bind/hla_motif_search_info.html), and all of the coefficient tables are available (http://thr.cit.nih.gov/cgi-bin/molbio/hla_coefficient_viewing_page). From what I can tell, the developers of that site made it very easy for anyone else to replicate the scoring function (which appears very simple) locally.

In addition to the warm, fuzzy feeling you'll get from not swamping their site, doing this locally has several other advantages, including:

• you're not dependent on their server (uptime, load)
• you don't have to write code to submit the data to their form (which is subject to format changes)
• you don't have to parse the HTML tables in the results page (which are subject to format changes)

I did a similar project a while ago. The time I saved by not having to write all the code to submit the input data via the form and parse the output (HTML pages) more than made up for the little time it took to create a module that contains the data and scoring function. In addition, I know that I'll never have to debug and recode anything because someone decided to change the format of one of the output tables.

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