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wandreopoulos / deeplasmid

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Hits to plasmid proteins #10

Open vanhoan310 opened 7 months ago

vanhoan310 commented 7 months ago

Dear authors,

I wonder how you define and compute (Boolean variable) a hit to database, e.g., plasmid_proteins?

Thanks

wandreopoulos commented 7 months ago

Hello, It uses minhashing in order to define hits to databases. Specifically sketch is used from bbtools to minhash a database and then map the kmers quickly. See: https://www.seqanswers.com/forum/bioinformatics/bioinformatics-aa/60935-minhash-sketch-a-tool-for-rapid-sequence-comparison

On Wed, Dec 6, 2023 at 12:22 AM vanhoan310 @.***> wrote:

Dear authors,

I wonder how you define and compute (Boolean variable) a hit to database, e.g., plasmid_proteins?

Thanks

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-- Thanks, Bill

William B. Andreopoulos, Ph.D. Joint Genome Institute LBNL