Hi, everyone!
I'm trying to estimate the expression levels of ERVs in human by mapping the reads on the consensus sequences.
I found a paper that used consensus sequences from Dfam, but I couldn't find the exact file.
I found some files 'hg38_dfam.hits.gz' and 'hg38_dfam.nrph.hits.gz' which had only location information without actual sequences.
Should I extract sequences using the location info, or is there other way?
Can someone give me some hints?
Thank you!
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written
by
mbk0asis
You can get the Dfam consensus sequences by downloading the HMM (i.e. DF0000558.hmm) and using hmmemit from the hmmer package:
hmmemit -c DF0000558.hmm > DF0000558.consensus.fasta
With the latest version of Dfam there is an API you can use to access the consensus sequences without downloading the HMMs. You would use the /families/{id}/sequence endpoint.
See http://dfam.org/help/api and https://dfam.org/releases/Dfam_3.0/apidocs/
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