HMM-based Model Library Search, SAM-T99

Warning: this page is in BETA release---bugs and changes may be frequent.


Please enter your email address (required)

Return email subject line (optional)

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

SAM-T99 Options

Search database:

email results

Last modified: November 11, 2000