HMM Library Search

This page offers the ability to compare a query sequence against our libraries of HMMs. It is part of a larger suite
of UCSC's HMM applications that are available on the web.

Note: this page is quickly becoming obsolete, having been superseded by the more accurate SAM-T99 model-library web page.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 HMM library search method

For a much quicker, but possibly less sensitive search, check the second box.
Summed method
Just score library

Step 4: Choose an HMM library


Step 5: 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:

   Email with questions and problems
   UCSC Computational Biology Group
   SAM Home Page
   Last modified: January 24, 1997
   Page designed by Christian Barrett,