How to calculate effective query length in TBLASTN
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8.1 years ago
islama • 0

Hi,

I am comparing a local alignment method with TBLASTN. In the BLAST report, I can't reproduce the effective query length value based on the given information.

For example, the report says:

Lambda K H
0.317 0.135 0.387

Length of query: 300
Length adjustment: 106
Effective length of query: 194

There is an equation in this link to calculate the effective query length.
Length_eff = MAX( Length_real - Lambda S / H , 1)

I would appreciate if someone can suggest how to get the S value from the given info or if there is anything I am missing here.

tblastn • 1.7k views
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