Target databases¶
The HMMER web service supports querying against a range of regularly updated sequence and HMM target databases.
Sequence databases¶
- Large, comprehensive sequence collection
- UniProt - Comprehensive resource for protein sequence and annotation data produced by the Universal Protein Resource consortium.
- Annotated sequences and determined 3D structures
- Representative Sets
- Representative Proteomes - Representative Proteomes (RPs) are determined by selecting one proteome from a representative proteome group containing similar proteomes calculated based on sequence co-membership in UniRef50 clusters. A Representative Proteome is the proteome that can best represent all the proteomes in its group in terms of the majority of the sequence space and information. RPs at 75%, 55%, 35% and 15% co-membership threshold are available as target databases. More information on Representative Proteomes is available. The data set also includes model organisms and viral reference proteomes as defined by UniProt. The complete proteomes database comes from PIR.
- Reference Proteomes - A set of proteomes from UniProt that gives broad coverage of the tree of life, and constitutes a representative cross-section of the taxonomic diversity to be found within UniProtKB. Produced by UniProt, in collaboration with Ensembl and the NCBI Reference Sequence collection.
The default database is UniProt reference proteomes.
Search provenance¶
Clicking ‘Search Details’ at the top of the result table reveals a box that provides details of the search, including the query sequence (if applicable) and information regarding 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.