Quick search

Paste in your sequence or use the example

Click the example link to add a sequence to the search box. The form requires a single sequence protein in FASTA format, with or without a header line. To search multiple sequences, (up to 500) click “Alternative Search Options” and then “Upload a file”.

Reference Proteomes UniProtKB SwissProt Pfam

Alternative search options

The HMMER web server: fast and sensitive homology searches. This site has been designed to provide near interactive searches for most queries, coupled with intuitive and interactive results visualisations.

Quickstart tutorial

Online documentation

Blog news August, 2015

hmmer.org is updating

hmmer.org is moving off of Janelia tonight, into the great cloud. You may see some flakiness as DNS nameservers update.

more...

Download HMMER

v3.3

Download Source

User's Guide: [PDF, pages]
Alternative Download Options

Recent papers

HMMER web server: 2018 update

S.C. Potter, A. Luciani, S.R. Eddy Y. Park, R. Lopez and R.D. Finn,
Nucleic Acids Research (2018) Web Server Issue 46:W200-W204. PDF

HMMER web server: 2015 update

R.D. Finn, J. Clements, W. Arndt, B.L. Miller, T.J. Wheeler, F. Schreiber, A. Bateman and S.R. Eddy
Nucleic Acids Research (2015) Web Server Issue 43:W30-W38. PDF

HMMER web server: interactive sequence similarity searching

R.D. Finn, J. Clements and S.R. Eddy
Nucleic Acids Research (2011) Web Server Issue 39:W29-W37. PDF