How to calculate effective query length in TBLASTN
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.
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