megablast returns hits not found by blastn?

Question

[7ehuang]

Hi all, It is my understanding that blastn is more sensitive (and thus finds more hits) than megablast (see here and here). However, when I compared my results from running blastn vs. megablast with the same exact inputs and parameters, I got 0 hits for blastn and thousands of matches for megablast (with e-value less than 0.001).

This seems really strange to me and I was wondering if anyone can think of a specific case in which megablast picks up hits that blastn can't pick? These are the commands I ran:

 blastn -query unique_31mers.fa  -db Homo_sapiens.GRCh37.dna.primary_assembly  -outfmt "6 delim=\t" -task 'megablast'  > GRCH37_blastn_31mers_mega.out

blastn -query unique_31mers.fa  -db Homo_sapiens.GRCh37.dna.primary_assembly -task 'blastn'  -outfmt "6 delim=\t"  > GRCH37_blastn_31mers.out

For context, the 31mers come from viral sequences.

Thanks!

Best, Elaine

Answer 1

[Mensur Dlakic]

It is not clear what result you got here because you are saying I got 0 hits for blastn and thousands of matches for blastn. I would expect that you are getting 0 matches with megablast because of its larger default word size.

Either way, you may want to try -task blastn-short as this is optimized for sequences shorter than 50 nucleotides.

[7ehuang]

Sorry about that, I mistyped. I meant to say I got 0 hits for blastn and thousands of matches for megablast (edited the original post). This is why I'm confused, because I also expected getting more matches with blastn than megablast. When I tried -task 'blastn-short', I also got 0 matches.