Using diamond instead of blastn

Open Pooryamb opened this issue 3 years ago • 3 comments

Hi,

Can't we use diamond for nucleic acid searching similar to blastn?

Mar 10 '22 04:03 Pooryamb

No a blastn mode is not supported at this time.

Mar 10 '22 12:03 bbuchfink

No a blastn mode is not supported at this time.

A, T, C, and G can represent both amino acids and nucleotides. What happens if we create a new scoring matrix whose mismatch/reward scores for ATCG are similar to mismatch/reward scores for nucleotides? Does it work for aligning DNA sequences?

Mar 10 '22 15:03 Pooryamb

No I don't think that would work well in practice without adapting a lot of other things in the algorithm.

Mar 15 '22 13:03 bbuchfink