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takaram / kofam_scan

CLI tool to annotate genes with KOfam
https://www.genome.jp/tools/kofamkoala/
MIT License
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How to compare multi hmm hits from one protein sequence #9

Closed lijie04 closed 4 years ago

lijie04 commented 4 years ago

Hi takaram,

Once hit score is over the threshold, then this hit will be marked as valid hit, resulted in some multi hits for one sequence. But, each hmm has its own threhold, which makes me a little bit confusing, as seems like these thresholds are not comparable to each other.

How would you suggest us to deal with multi hmm hits from one protein sequence?

takaram commented 4 years ago

There may be many ways to interpret such hits. For example, you can use "F-measure" in ko_list, because it reflects the reliability of the HMM (reliable when F-measure close to 1).