search

asbschmidt / CUDASW4

CUDASW++4.0: Ultra-fast GPU-based Smith-Waterman Protein Sequence Database Search
Apache License 2.0
28 stars 5 forks source link

Nucleotide sequences? #4

Open vladimirkhramkov opened 10 months ago

vladimirkhramkov commented 10 months ago

The new version of CUDASW 4.0 claims to support only protein chains. What needs to be done to be able to search in the nucleotide database?

Sherman-1 commented 7 months ago

I would be really glad if there was a nucleotide substitution matrix ! From what I see in files options and types there are only BLOSUM. Would it be possible to add some DNA substitution models ?

vladimirkhramkov commented 7 months ago

I have implemented this idea in my fork. I have added DNA and NUC4.4 matrices and new parameter -type for makedb and align programs.