[Biojava-l] [Biojava-dev] Does biojava can calculate evalue ?

Richard Holland holland at eaglegenomics.com
Sat Aug 30 19:00:37 UTC 2008

BioJava does not include functions to calculate e-values - nor should
it, as the e-value you wish to calculate depends entirely on the
search algorithm the e-value is associated with. You will need to
determine an algorithm of your own that will calculate e-values based
on your own knowledge of the sequence search algorithm that you have

The simplest form of e-value is a function of the query sequence
length and the total length of the sequences available to search. More
complex forms include such things as analyses of the content of the
sequences and the percent identity of the match, or in fact anything
that may be appropriate and significant to the way the search
algorithm works. It's basically up to you how to define it.

Good luck!


2008/8/30 simpleyrx <simpleyrx at 163.com>:
> Dear experts,
>  I develop a sequence search program. Now , my program can calculate the score value ,and I want to provide a expectation value ( like blast evalue) to user. I do not know how to do in this step. Can biojava do it ? Thank you in advanced.
> --
> Student
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Richard Holland
Finance Director
Eagle Genomics

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