Protocol Online logo
Top : New Forum Archives (2009-): : Bioinformatics and Biostatistics

Selecting sequences in NCBI with > 95% Query coverage and >90% identity - (Apr/20/2014 )

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.

-Inbox-

Just blast them...

http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_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.

-pito-

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

-Inbox-

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.

-pito-