HMM-based Sequence Query

This page offers the ability to perform remote protein homolog searches using HMM technology. It is part of a larger suite
of UCSC's HMM applications that are available on the web. If you are familiar with BLAST searching, then you understand the functionality of this page.

Note: this page is quickly becoming obsolete, having been superseded by the more accurate and more featureful SAM-T99 web page.

Step 1: Enter email address and optional subject line

Please enter you email address ( required )
Return email subject line (optional)

Step 2: Enter one sequence

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.
Cut and paste your sequence here, ...

or specify the sequence-containing file on your system here.

Step 3: Choose database to search for homologs

PDB (quick)
SWISSPROT (a couple hours)
971 SCOP domains

Step 4: Choose threshold for reporting database hits

If you want to include more remote, or weaker scoring, sequences in the
final report, choose a cutoff value that is less negative. The more negative
the cutoff, the more strict you are being about what you will consider
as a "hit".
NLL-NULL score cutoff:

Number of alignments to include:

Acquisition of Alpha workstations and AlphaServers was made possible by
NSF grant CDA-9115268, and a donation from

Email sam-info@cse.ucsc.edu with questions and problems
UCSC Computational Biology Group, SAM Home Page
Last modified: January 24, 1997
Page designed by Christian Barrett, cbarrett@cse.ucsc.edu