EMBOSS explorer


Build a profile HMM from an alignment. (read the manual)

Unshaded fields are optional and can safely be ignored. (hide optional fields)

Input section

Select an input sequence. Use one of the following three fields:

  1. To access a sequence from a database, enter the USA here:
  2. To upload a sequence from your local computer, select it here:
  3. To enter the sequence data manually, type here:
HMMER dirichlet prior file (optional):
HMMER null model file (optional):
HMMER matrix file (optional):
Weighting for PAM.
Required section
Name for this HMM.
Select preference
Advanced section
Threshold to switch to position-based weights.
Architecture prior
Write HMM as binary.?
Work in fast mode?
Fast mode control
Specify model by hand.?
Cutoff ID threhold
Turn off the effective sequence number calculation.?
Probability control for local entries
Probability control for exits
Select weighting
Output section
Run section
Email address: If you are submitting a long job and would like to be informed by email when it finishes, enter your email address here.