Yeah, blastn -task blastn-short
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Short sequences against short sequences alignment
Hi,
I have thousand short sequences (~30 bp) in fasta format and I want to compare all of them against a database of short sequences (also around 30 bp), which are also in a fasta format.
I know blastn and USEARCH can probably handle such comparisons, but have you some advice?
Thank you
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1 answer
Why not just try blastn? It sounds like it shouldn't take a long time to build a BLAST database and query it.
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A little up!
Any advice?
Can you provide some additional information?
Are these sequences homologous or not so (if not what % identity on average)? Are you ok with allowing gaps in alignment and do you want to the alignments to be global (end-to-end)?
Depending on your answer, blat may work. You could also give BBMap a try.