Short sequences against short sequences alignment

Question

[a.vincent.0312]

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

[a.vincent.0312]

A little up!

Any advice?

[GenoMax]

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.

Answer 1

[Mikael Huss]

Why not just try blastn? It sounds like it shouldn't take a long time to build a BLAST database and query it.

[5heikki]

Yeah, blastn -task blastn-short