HMMER Menu
This menu is available if hmmbuild tools have been installed and configured in the
HMMER Preferences panel.
hmmbuild
Run hmmbuild to create a Hidden Markov Model profile of your sequence alignment or sub-groups.
The consensus sequence for the computed profile is inserted as the first sequence of
the alignment (or group) for which hmmbuild is run.
Jalview also computes and displays an annotation below the alignment, showing
the information content of each column.
This is calculated as the sum over residue symbols of
match emission probability * log(match emission probability / background frequency) / log(2)
where the background frequencies are taken from (tbc: where? not https://www.ebi.ac.uk/uniprot/TrEMBLstats)
- Edit settings and run...
Choose whether to run hmmbuild for the whole alignment, or all or selected groups, or both
(default is the alignment).
Optionally enter a name to give the HMM profile consensus sequence
(default is "Alignment" or group name, with "_HMM" appended).
Use Reference Annotation: select this option if your alignment has an RF reference annotation,
and you wish to constrain the HMM profile to it (hmmbuild option '--hand').
- hmmbuild with default settings
Runs hmmbuild for the whole alignment.
hmmalign and hmmsearch require an HMM consensus sequence to be selected first.
To do this, right-click on the name of an HMM sequence added by hmmbuild, and 'Select HMM'.
The alignment will be with respect to the HMM profile for the consensus sequence.
hmmalign
Run hmmalign to align selected sequences (or the whole alignment) to a selected HMM profile.
- Edit settings and run...
Choose whether to 'trim non-matching termini' - hmmalign option '--trim'.
- hmmalign with default settings
hmmsearch
Run hmmsearch to use an HMM profile as input to search a sequence database.
- Edit settings and run...
- tbc: choose database
- tbc: automatically align
- tbc: return accessions
- tbc: number of results
- tbc: sequence eValue cutoff
- tbc: domains eValue cutoff
- hmmsearch with default settings
- Add database
Browse to select a local sequence data file to be searched