Help Contents:
  1. Contacting and citing us
  2. HMMER3 algorithms
  3. Supported target databases
  4. Search Parameters
  5. Results
  6. Application programming interface

Note: These help pages are primarily designed to give users a very brief introduction to HMMER, sufficient such that the user will have a better understanding of the website search methods and ensuing results. They do not describe the details of profile hidden Markov models (HMMs) in the use of sequence analysis.

Contacting and citing us

Citing us

If you have used the HMMER website, please consider citing the following reference that describes this work:

HMMER web server: interactive sequence similarity searching
R.D. Finn, J. Clements, S.R. Eddy
Nucleic Acids Research (2011) Web Server Issue 39:W29-W37. PDF

Staying Informed

As with many scientific websites, this web site is in constant flux. Most of the changes are related to updates to the underlying target databases. In addition, we are constantly developing new features and fixing minor bugs to improve the site. The following are aimed at keeping users abreast of changes:


Your questions are important to us. Please use the email address at the bottom of the page for any questions regarding the use of the HMMER software or the servers. Our helpdesk is currently a simple mailing list. We will respond as quickly as possible to all questions, but until we get a dedicated person running the help-desk, our responses may be a little slow. Software bug reports will typically be dealt with by Sean Eddy, but may get deferred to others within the HMMER project team. To expedite our response to your questions, please provide us with as much information as possible so that we can recreate the problem, but equally do not write pages and pages. Useful things to include are:

Without these pieces of information we have to guess or send mails back and forth to determine the cause of the issue. Many questions are also covered in these help pages and in the HMMER documentation, so it may be worth browsing them first before sending us an e-mail.

We expect more questions about the new servers. These questions will normally be addressed by Rob Finn and Jody Clements. If you like or do not like what we are doing, then please get in touch. Also, if there are new features that you would like to have added to the server, then drop us a line and we will see what we can do!