EMBOSS explorer


Search a sequence database with a profile HMM (read the manual)

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

Input section
HMMER hidden markov model file:

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:
Required section
Number of alignments
Additional section
E-value cutoff
Bit score cutoff
Advanced section
Calc E-value for fixed database size.
Use HMMER 2.1.1 output format.?
Number of CPUs
Use Pfam GA (gathering threshold) score cutoffs.?
Use Pfam TC (trusted cutoff) score cutoffs.?
Use Pfam NC (noise cutoff) score cutoffs.?
E-value domain cutoff
Bit score domain cutoff
Use forward algorithm?
Turn off second null model?
Use parallel virtual machine?
Use XNU filtering?
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.