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Selecting sequences in NCBI with > 95% Query coverage and >90% identity


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#1 Inbox

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Posted 20 April 2014 - 09:28 PM

Hello,

      I have following sequences for which I want to BLAST and see result only for sequences showing > 95% Query coverage and >90% identity?

 

Sequences

>1
CTTTGTCTTCCCCTATGTCATCCTCAATCTCTATGAAAGCAACAC 
>2
CTATGTCATCCTCAATCTCTATGAAAGCAACACCGCTACCATAGA
 
 
Can you please Suggest how can I select them in NCBI BLAST. Thanks.


#2 pito

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Posted 21 April 2014 - 12:48 AM

Just blast them...

http://www.ncbi.nlm....K_LOC=blasthome

 

I dont understand your problem.

 

It will automatically adapt for short sequences and do a megablast (normally also automatically set).

 

It will give you some results and the top results are the ones you want.


If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.


#3 Inbox

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Posted 21 April 2014 - 08:08 PM

Thanks pito. I got answer. In BLAST result we may not adjust query coverage. Identity we can fix by formatting option after BLAST.



#4 pito

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Posted 21 April 2014 - 11:18 PM

Thanks pito. I got answer. In BLAST result we may not adjust query coverage. Identity we can fix by formatting option after BLAST.

yes indeed.

 

but it automatically gives you the best homologies.


If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.





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