Dfam

Retrieve Hits

Retrieve pre-calculated Dfam matches for up to 50Kbp ranges of genomic sequence. More...

Pre-calculated matches are from Dfam + nhmmer searches against dfamseq, which contains reference assemblies for human [hg38], mouse [mm10], zebrafish [danRer10], worm [ce10], and fly [dm6]

By default, redundant profile hits (RPH) will be removed as indicated by the checkbox. You can optionally make the search specific to a model by entering the Dfam accession or identifier.

The search will analyze both strands between the co-ordinate range, fetching both Dfam model matches that score above the gathering threshold and Tandem Repeat Finder (TRF) matches.

Organism:
Chromosome:
Range:: Start: End:
Dfam entry (optional):
Remove redundant profile hits:

Keyword Search

Sequence Search

Find Dfam matches to your sequence of interest. Paste your nucleotide sequence into the box below, to have it searched for matching Dfam entries. More...

This search comprises of two parts, a search of the sequence against all of the Dfam models and a search against TRF, the tandem repeat finder. Overlapping Dfam matches (near perfect overlaps) are automatically removed as part of the search method, in order to remove the model redundancy.

The recommended method of searching is to put the source organism of the query sequence, and let the software determine the best cut-off for each model, where the more stringent thresholds will be used for sequences where the source organism does not match the model specificity. Otherwise the more liberal gathering thresholds will be used. Alternatively, you can specify an E-value to use for each model. The search system can be downloaded and run locally. There are more details of both the search and dfamscan.pl in the help section.

Sequence

Query Organism

Cut-off

Dfam curated threshold
Use E-value

E-value