DNA-DNA alignments?

[raw937]

Any thoughts on this?

[rvaser]

There is a branch dna_dev which implements some kind of DNA support, but I do not have the time at the moment to deal with it properly.

[raw937]

Long time my brother! I hope you are well. Thank you for your reply. I feel sword did nucleotide-protein (query/database) very well. Is that true?
Also, how big of a database have you tested?
What would you recommend to make the dna_dev part work?

[rvaser]

If I recall correctly, you have been testing nucleotide-protein alignments but I am not sure what was the outcome. Sword was developed for protein-protein search only, and I would need to overhaul the whole code in order to make it work better on DNA. Unfortunately, I do not have time at this moment for this.

Sorry for my late reply!
Best regards,
Robert

[rvaser]

You can also check out https://github.com/ivujevic/tachyon, much faster aligner which supports DNA sequences.

[raw937]

Hello Robert. I don't see where tachyon does blastn? Only blastx right? I need a fast blastn.

[rvaser]

Why not use https://github.com/lh3/minimap2 then? You can search the issues tab there for blastn.