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You may either cut and paste your seed alignment 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. You can omit the seed alignment and provide only unaligned sequences in the "unaligned" box below.
Cut and paste your seed alignment here, ...
or specify the seed-alignment-containing file on your system here.
You may either cut and paste your unaligned homolog sequences 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.
Cut and paste your homolog sequences here, ...
or specify the homolog-sequence-containing file on your system here.
This page offers the ability align a set of protein sequences or to refine an existing protein seed alignment using HMM technology. It is part of a larger suite of UCSC's HMM applications that are available on the web. You may provide a seed alignment (or sequence), unaligned sequences, or both. Please refer to the method used by this web page as SAM-T99(tuneup).
The methods of this web page are part of the current release of SAM ---those who have large amounts of data (or proprietary data) should get SAM licenses and run the scripts locally. The online documentation should provide complete instructions for using the scripts.
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-info@cse.ucsc.edu.
return T99 alignment in format(s): A2M Pretty Align HTML Sequence Logos
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Email sam-info@cse.ucsc.edu with questions and problems
UCSC Bioinformatics Group
Target 99 developed by Kevin Karplus, karplus@cse.ucsc.edu
Page designed by Spencer Tu, stu@cse.ucsc.edu
Last modified: October 28, 2000