[Bioperl-l] E-value of a combined alignment?

[Richard Harrington]

Hi,
>
> Hi folks,
>
> 	I am aligning mRNAs against human genome using ungapped tblastx. I
> got a bunch of HSPs with different e-values. I can observed that some of
> them should be in the same group because they are exons of a gene. But
> then what is the e-value of all these HSPs combined?
>
> 	I know the formulas of e-value and bit score for BLOSUM62:
>
> Let S' be bit score, S be score, e be e-value, m be the length of HSP, n
> be length of database.
>
> S' = (0.318 * S - ln(0.135)) / ln(2)
>
> e = m * n / (2^(S'))
>
> 	I am guessing the formula for the e-value of
> non-overlapping combined e-value to be:
>
> S'' = (0.318 * sum_of_S - ln(0.135)) / ln(2)
>
> e' = sum_of_m * n / (2^(S''))
>
> 	Is this correct? Or do you know the right way to calculate it?
>
> Thanks in advance.
> Yee Man
>

another good place to post this query might be the new 'Sequence Searching
mailing list' (ssml).

http://bioinformatics.org/mailman/listinfo/ssml-general

Cheers,

Richard

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_______________________________________________

Richard Harrington,
HUS Graduate Vice-President,
Homerton College.

PhD student,
Bioinformatics Group,
MRC-Dunn Human Nutrition Unit,
Cambridge University.

e-mail: rah at mrc-dunn.cam.ac.uk
telephone: +44 (0) 1223 252861
_______________________________________________