A question about classification #5
Description
Dear developers,
I have been running metagenome hydrogenase annotation and classification as follows:
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hmmsearch with strict cut-offs: [FeFe]: 50, [NiFe]: 120, [Fe]: n/a.
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diamond blastp search with strict identity cut-offs. Command were set as recommended: "diamond blastp --ultra-sensitive --max-target-seqs 1 ..."
I can't help but noticed you have recommended the blastp report of ONLY ONE hits with parameter"--max-target-seqs 1". It seems like that if a sequence whose best hit in diamond blastp database failed the final class-specific identity cut-offs would be discarded for classification. But it is possible that a candidate hydrogenase of other groups (such as group 3) returned its best hit as group 4 failed to be recognized due to the "ONLY ONE HIT" comparison setting?
Please, a little guidance would be deeply appreciated.