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soda examples



The source code for this example can be found on GitHub

Dfam-SODA was developed to visualize transposable element annotations from the Dfam database. This application is also hosted (with additional features that integrate with the Dfam platform) on the Dfam website.

From the Dfam site:

Retrieve pre-calculated Dfam matches for ranges of genomic sequence.

Up to a 1Mbp range can be retrieved at a time, but 100Kbp or smaller is recommended for readability and performance depending on your machine.

Pre-calculated matches are from Dfam + nhmmer searches against dfamseq, which contains reference assemblies for selected genomes covered by families in Dfam.

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.
remove redundant profile hits