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Published 20 hours ago • verified publisher icon rvaser

DNA-DNA alignments?

Open raw937 opened this issue 3 years ago • 6 comments

Any thoughts on this?

raw937 avatar Mar 11 '21 18:03 raw937

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.

rvaser avatar Mar 12 '21 03:03 rvaser

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?

raw937 avatar Mar 12 '21 03:03 raw937

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 avatar Mar 18 '21 03:03 rvaser

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

rvaser avatar Mar 18 '21 04:03 rvaser

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

raw937 avatar Mar 02 '22 22:03 raw937

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

rvaser avatar Mar 05 '22 08:03 rvaser