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Last pushed: 2 years ago
Short Description
Run hmmsearch with parameters
Full Description

debian-hmmsearch2

run hmmsearch in HMMER package with parameters(profileHMM and FASTA formatted database file).

example: docker run -it bonohu/debian-hmmsearch2 PF00081 \
ftp://ftp.ensemblgenomes.org/pub/metazoa/release-25/fasta/bombyx_mori/pep/Bombyx_mori.GCA_000151625.1.25.pep.all.fa.gz

contents of 'hmmsearch.sh' script in Dockerfile is as follows.

#!/bin/sh

get hmm

wget -O hmm.hmm http://pfam.xfam.org/family/$1/hmm

get DB

wget -O db.fa.gz $2

run hmmsearch with parameters

hmmsearch hmm.hmm db.fa.gz

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bonohu
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