Hi Everyone,
In stand-alone blast, I'm blasting several thousands of ~450nt long sequences against one short ~50nt long motif sequence to find the sequences that has this ~50nt motif. In blastn output I get couple of hits with >90% (and alignment length = 50) So my questions are-
- Why I'm not getting the hits below 90% identity (like sequences that has 85 or 70% identity to the motif seq)?
- Is there other efficient way/tool available to find the sequences from the data that has my seq of interest in it?
I'm new to blast and bioinfo in general so any help/inputs would be highly appreciated!
Thanks very much!
For some weird reason, I've seen legacy BLAST's blastall work better on the shorter nucl sequences than blast+ 's blastn. Have you tried blastall?
Also, I think 70% of 50 nucl (30 nucl) might too short of a match for BLAST to consider, and you might wanna tweak parameters a bit.
Thanks Ram for your reply. Haven't try the blastall yet but will try that now. And which parameters exactly I will have to change?
Few more Qs-
Again, thanks.
R