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Correct percent identity based on gene coverage.

Hello,

When I run blastn on a sequence of a specific gene it returns percent identity. However, I would like to be able to correct for the coverage of the gene (How well the read covers the identified gene targeted by the primers). For example, if the coverage of the gene is 98% I would like to correct the % identity for the missing part of sequence. Could someone please suggest what formula to use?

Thanks

alignment
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updated by Joe Joe • written by genya35 • genya35

1 answer

It should be sufficient to simply scale ID by coverage as a percent, e.g:

Normalised ID = ID x (Coverage / 100)

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written by Joe Joe

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