[Biodevelopers] Blast not symmetrical?

[Michael Nuhn]

Hello, Malay!

> This is a very well known phenomenon. You can read more about it here:
>
> http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html
>
> Why this appears to be counter-intuitive is because people mistake
> BLAST scores (a sort of bit value) with alignment score. The raw
> alignment score will be same for both the alignments.

Ok.

> But Blast bit score is then calculated from the raw alignment
> score taking into consideration of background distribution
> of the amino acids of the query sequence.

The link you sent shows how the bit score (S') is derived from the raw score
(S):

S' = ( lambda * S - ln K) / ln2

Where the value of lambda is only derived from the scoring matrix and K is a
constant that I don't understand.

Where does the background distribution of the amino acid (or in my case DNA)
sequence of the query come in?

Regards,
Michael.

--
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Dipl.-Inform. Michael Nuhn
Bioinformatik
Zentrum für Nanostrukturtechnologie und
Molekularbiologische Technologie

+49 (0)631 - 205 4334
nuhn at rhrk.uni-kl.de
http://nbc3.biologie.uni-kl.de/
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