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You may either cut and paste your sequence in the box below or upload it from a file on your local system. Sequences must be in a readseq-compatible format---we recommend FASTA format. You may also use a multiple alignment as a seed, which must be in a2m format.
Cut and paste your sequence here, ...
or specify the sequence-containing file on your system here.
Further options appear below.
This page offers the ability to score a query sequence with a library of HMMs for proteins of known structure. It is part of a larger suite of UCSC's HMM applications that are available on the web. For an advanced search with more options, see the SAM-T99 query web page. More details on the methods used can be found in an HMM tutorial, though that tutorial talks about the predecessor SAM-T98 method, which differs in several parameter choices.
You can check the SAM-T99 server queue status here . (Local users at UCSC check here .)
Please read the explanation of common errors on our SAM-T99 Frequently-asked Questions page. If you do not find a solution to your problem there, please inform us at firstname.lastname@example.org.
Last modified: November 11, 2000