gravatar for vishalchanda364

2 hours ago by

Hello all,
While working on the step, where I need to align my reads to the pVOG (Prokaryotic Viral orthologous groups) database using HMMER, the e-value I selected was 1e-5 in the command hmmscan --noali -E 1e-5 --tblout table.txt databse.hmm input.faa > output.fa
and likely wanted to see the result as single hits with that particular hit (as I have new to bioinformatics) but now the result which I got looks like this,

target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target

VOG4724 - k141_29440_2 - 5.2e-08 - 32.1 - 4.4 - 7.3e-08 - 31.7 - 4.4 1.3 1 1 0 1 1 1 1 -

VOG7442 - k141_19630_1 - 1.4e-20 72.9 0.0 1.9e-20 72.4 0.0 1.1 1 0 0 1 1 1 1 -

VOG0348 - k141_19630_1 - 3.1e-08 31.7 0.3 7.6e-05 20.4 0.1 2.3 2 1 0 2 2 2 2 -

VOG0083 - k141_19630_1 - 1.5e-07 29.9 0.8 0.0033 15.5 0.0 2.0 2 0 0 2 2 2 2 -

VOG8462 - k141_19630_1 - 1.5e-07 29.7 0.0 1.9e-05 22.8 0.0 2.1 2 0 0 2 2 2 2 -

Now in the first sample it has only one hit so I can choose easily, but how do I get the best hit from the second sample. and how can I curate it from that big table so that I have only the best hit file with me.?

Please help.

thanks, VISHAL



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