Service Update: Temporary reduction of features

To meet the ongoing demand for HMMER searches, as well as allow us to update the underlying sequence databases to more recent versions, we have accelerated the release of a new underlying search system. However, we have yet to completely address the issues of making large sequence alignments based on search results, as required by jackhmmer. As the generation of these alignments currently cause the web servers to crash, we have temporarily suspended jackhmmer searches. Also, based on current usage patterns we have omitted some target sequence databases. We anticipate returning most, if not all functionality, in the near future, but in the meantime please bear with us as we continue to upgrade the infrastructure behind the HMMER servers.

protein sequence vs protein sequence database

Paste a Sequence | Upload a File | Accession 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 'Upload a file'.

Accession / ID Lookup

Upload a file

- and provide an (optional) -

Email Address

Sequence Database

Choose one of the following target databases for your query to be searched against. The databases vary substantially in size and the amount of functional annotation.

Frequently used databases:

Current database selection:

Cut-Offs

There are two different ways of controlling which target sequences match your query.
E-value:Control both significant and reporting thresholds for the entire sequence and each hit, 10≥x>0. May be entered with scientific notation.
Bit score:Control both significant and reporting thresholds for the entire sequence and each hit, x>0.

E-value

Significance E-values: Sequence Hit
Report E-values: Sequence Hit

Bit score

Significance bit scores: Sequence Hit
Report bit scores: Sequence Hit