HMMER biosequence analysis using profile hidden Markov models

Help Contents:

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

Target sequence databases

We currently support the following sequence databases searching against:

• Large, comprehensive sequence collections
• NR - Non-redundant proteins from GenBank CDS translations, RefSeq Proteins, PDB, SwissProt, PIR and PRF - produced by NCBI.
• UniProtKB - comprehensive resource for protein sequence and annotation data produced by the Universal Protein Resource consortium.
• Annotated sequences and determined 3D structures
  • Swiss-Prot - Manually review, high quality protein sequence and functional annotation - produced by UniProt.
  • PDB - sequences with an experimental determined structure.
• Metagenomic and environmental sequences
  • Unimes - Specific repository for metagenomic and environmental data produced by UniProt.
  • env_nr - Translations from env_nt (contains DNA sequenced directly from the environment with all organisms mixed together) - produced by the NCBI
• Representative Sets
• Complete Proteomes - representative proteomes that are selected from clustered proteomes (55% co-membership threshold). The data set also includes model organisms and viral reference proteomes as defined by UniProt. The complete proteomes database comes from PIR.

The default database will be either NR or UniProtKB depending on the location of the incoming HTTP request.

Target profile HMM database

In all cases of searching against a profile HMM database, the library of HMMs corresponds to Pfam.

Search provenance

At the end of each results page there is a Search Details link. Clicking the link reveals a box that provides details of the search that has just been performed and will show the query sequence (if applicable). Furthermore, important information is contained about the date/release of the target databases, which should be recorded for future reference when trying to recreate the results, discussing with colleagues or reporting bugs.