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superseded by the more accurate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
PDB
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:
