BLAST results (was RE: [Biodevelopers] Blast not symmetrical?)

[Michael Nuhn]

Hi, Dave!

>Perhaps you can explain this to me.  I searched an
>AA string against the rat genome.  I got a poor hit
>(e-value about 50), so I decided to see if there was
>a homologous gene, and I searched against all genomes.
>Instead of returning the same hit (or better), but best hit
>I received was about 360!  Why is this?  I'm confounded.

The e-value tells you the number of alignments expected at random with this
score.

If you search a larger database, you would expect more random hits. That is
why you e-value got worse when you were searching a larger database.

Cheers,
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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