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Tutorial for using the COMER web server

Users are encouraged to refer to the Help page to familiarize themselves with the services provided by the COMER web server.

The main page of the COMER web server is where input data can be entered. Enter queries in the text field. The separator line “//” indicates the end of an individual query, which can represent a sequence, plain or in FASTA format, an MSA in aligned FASTA, STOCKHOLM, or A3M format, or a COMER2 profile.


Select target profile databases, sequence search methods for building more informative multiple sequence alignments (MSAs):

Main options

Check advanced options:

Advanced options

Hitting the Submit button places a job in the queue:

Submit button

The job is running. The progress of the job appears:

Job status page

The job has finished, and the list of links to individual results pages, one for each query, appears:

List of results

For each query, results summary and table are displayed. Clicking on the schematic alignment or table row number displays the result alignment:

Query results: summary

Each results page shows the profile-profile alignments between a query and the identified proteins along with predicted secondary structures, which help visually assess how well structural features align. Alignment statistics that accompany each alignment provide additional criteria for assessing the closeness of the aligned pair or compositional similarity (relatively low values of λ):

Query results: alignment

Select multiple pairwise alignments:

Alignment selection by E-value

Construct an MSA based on profile-profile alignments:

MSA construction button

Constructed MSA

Or generate 3D structural models, one for each selection, with a click of a button:

Generate single-template 3D models button

Generated single-template 3D models