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What is Hit Fraction and how is the Hit fraction determined from blast output

Does anyone know any means of checking the hit fraction from a blast output? And what does hit fraction mean particularly? Is this the percentage of sequences that just have the highest score and similarity to the query.

Would appreciate clarification and help?

blast
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updated by h.mon h.mon • written by apulunuj • apulunuj

1 answer

You don't show any examples of output you want to interpret, it would be helpful if you did. When performing orthology searches, hit fraction is defined as:

The simplest method is to filter out BLAST results that do not meet a minimal coverage percentage for either sequence (“hit fraction” [...]

Reference: Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics.

Or:

[...] hit fraction, which is the set union of the sets of locally aligned sites (hits) reported by BLAST.

Reference: Inferring angiosperm phylogeny from EST data with widespread gene duplication.

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written by h.mon h.mon

I was looking for the definition as you explained or pointed out above. Thank you for the references it helped.

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written by apulunuj • apulunuj

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