Paste a Sequence | Upload a File | Accession Search
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'.
- and provide an (optional) -
Set the profile HMM database that your query will be searched against.
Protein Families
There are three different ways of controlling which HMMs match your query. E-value: Control both significant and reporting thresholds for the model and each hit, 10≥x>0.May be entered with scientific notation. Bit score: Control both significant and reporting thresholds for the model and each hit, x>0. Gathering: Use the HMM database defined significance thresholds.
Use the gathering threshold.
Note: The Gene3D, Superfamily, and PIRSF databases will ignore custom cut-off parameters since they use a post processing step that involves preset thresholds.
Under some circumstances, hits can be lost due to the fact a sequence, or regions of a sequence, are omitted due to bias composition. You can turn this filter off, but it will slow down your searches.
HMMER