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

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

blast alignment sequence
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updated by Antonio R. Franco Antonio R. Franco • written by seta seta

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.

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written by GenoMax GenoMax

1 answer

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

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written by Antonio R. Franco Antonio R. Franco

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