re taxonomic information in the metaphlan database

[KM Tsui]

Hello,

I have downloaded the metaphlan database <mpa_v296_CHOCOPhlAn_201901.fna> in order to use the "marker " sequences for oligo design.

But the sequences have no taxonomic information, such as family and genera ...

How can I find those information or did I download the complete database?

I will appreciate for some advice. Thanks,

regards,

Clement

[Francesco Beghini]

Hi Clement,

Each marker has included in the id the NCBI taxonomy id of the species (e.g. 671232__F5U0A1__C6A26_01825 --> 671232 is the taxid).

You can get also the full lineage from the pkl file after loading it into a (i)python session and looking into the 'markers' section.

Let me know if you have any more questions.

Best,

Francesco

Francesco Beghini

PhD Student - Laboratory of Computational Metagenomics

Department of Cellular, Computational and Integrative Biology - CIBIO

University of Trento

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