Why there is a big difference for blastn and blastx results of a given sequence

Question

[seta]

Hi all,

I locally performed blastx analysis for some sequences using ncbi-blast-2.2.30+ package. Now, when I randomly select one sequence and subject to on line NCBI tool for blastx, the results are similar to what I already found, but when I do the same work for blastn, it says that No significant similarity found. Could you please let me know why there is such a difference?

Thanks

[natasha.sernova]

I know that blastx searches in 6 frames. This may be the reason.

http://blast.ncbi.nlm.nih.gov/Blast.cgi here there are some datails about all blasts.

[GenoMax]

Were you replicating local settings (and/or database) for the blastn @NCBI exactly? At times blastn @NCBI will reconfigure settings depending on length of query sequences etc (it does warn you but it is hard to find out exactly what was changed). @NCBI also uses some custom databases that are not available for download by default.

Answer 1

[Antonio R. Franco]

You don't mention the kind of blastn search you used, whether it was a megablast (search for very similar sequences), a discontinuous Megablast able to find some related sequences or the setting that allow you to find even less related sequences