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4.7 years ago
vishalchanda364
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20
Hello, I was working on a metagenomic data following the pipeline explained by Skoporov et al., 2019 there in a step of identifying temperate bacteriophage, they have used hmmscan from HMMER, I followed the steps as explained and got a table output.
VOG11081 - k141_49172_1 - 1.2e-07 29.8 0.1 1.2e-07 29.8 0.1 1.0 1 0 0 1 1 1 1 -
VOG0025 - k141_49172_1 - 1e-06 28.0 0.1 1.1e-06 27.9 0.1 1.0 1 0 0 1 1 1 1 -
VOG0092 - k141_21860_1 - 4.4e-10 38.3 0.0 4.4e-10 38.3 0.0 1.1 1 0 0 1 1 1 1 -
VOG8599 - k141_21860_1 - 2.3e-08 33.2 0.1 5.7e-08 31.9 0.1 1.8 1 1 0 1 1 1 1 -
VOG0384 - k141_49174_1 - 5e-15 54.3 0.0 5.4e-15 54.1 0.0 1.0 1 0 0 1 1 1 1 -
VOG5733 - k141_10934_1 - 1.3e-07 30.9 0.2 1.5e-07 30.7 0.2 1.1 1 0 0 1 1 1 1 -
Something like this. Now I know that I can retrieve the best hit form the table and save the sequence from my sequence file, but how may I get the exact name of the organism, the sequence belongs to from the reference .hmm file? Please help.!
Thanks, Vishal