Question: which factors help to select positive blastx result?
gravatar for Kurban
5.1 years ago by
china/Urumqi/xinjiang academy of animal scinces
Kurban170 wrote:

hello guys!
i have BLASTXed a query file (which contain more than 140000 nucleotide sequences) with a db file (which contain more than 1400 polypeptide sequences). got the blasted query sequences around 20000 (with e-value 3) , then i change e-value to 5 still got more than 15000 aligned sequences . when i checked the identity(%) of them, there r more that 2000 sequences that their identity smaller than 30.
when i analysis the blastx result  which factors should i consider?
should i select 3 or 5 for e-value?
what % of the identity could be the threshold for blastx result?

thank you in advance.


blast • 1.1k views
ADD COMMENTlink modified 5.1 years ago by RamRS25k • written 5.1 years ago by Kurban170
gravatar for RamRS
5.1 years ago by
Houston, TX
RamRS25k wrote:

Lower e-values are always better. E-value is the probability that you're seeing a match just by chance, so e-value of 3 should be better (though I normally use e-values that are more near 1e-3 than 3).


I'd also suggest throttling identity at ~75%, but this depends on the query and the subject more than just the program.

ADD COMMENTlink written 5.1 years ago by RamRS25k
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