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steineggerlab / Metabuli

Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
GNU General Public License v3.0
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Question regarding databases #65

Closed stas-malavin closed 6 months ago

stas-malavin commented 6 months ago

Hi,

Could you please clarify—to build a database, do I need both nt and aa seqs, or does metabuli translate nucleotides by itself? If it translates, can I specify the translation table?

And the databases themselves are not MMSeqs2 databases, right?

Thank you

jaebeom-kim commented 6 months ago

Thank you for reaching out. Nucleotide sequences are enough to build a DB. Metabuli translates it to build DB. You cannot specify the translation table. The standard table is utilized for all. Since it handles metagenomic data, query reads have to be translated with standard codons. To best match the query, reference DB is also built using standard table.

Metabuli DB and MMseqs2 DB are different.

Thanks again!

From: Stas Malavin @.> Sent: Tuesday, May 21, 2024 5:02:21 PM To: steineggerlab/Metabuli @.> Cc: Subscribed @.***> Subject: [steineggerlab/Metabuli] Question regarding databases (Issue #65)

Hi,

Could you please clarify—to build a database, do I need both nt and aa seqs, or does metabuli translate nucleotides by itself? If it translates, can I specify the translation table?

And the databases themselves are not MMSeqs2 databases, right?

Thank you

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stas-malavin commented 6 months ago

Thanks for the elaborated reply!