small representative database
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17 months ago
lagartija ▴ 90

Hi,

I wonder if it exists somwhere a representative database that if smaller than refseq. I would need genomes from different phylums of Bacteria, Archaea, Viruses and Eukaryotes and that I can download directly on my computer. This would probably result very useful for anyone who wants to run some pre-tests before using refseq (too big) or metagenomic datasets (uncertain taxonomy)

Thank you very much !

taxonomy data genomes proteomes • 277 views
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If you need representative metagenomic databases then take a look at those provide by kaiju (see box on left of page).

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17 months ago
Mensur Dlakic ★ 12k

UniProt has all kinds of reference databases, including those clustered at 50% and 90% identity. Files related to taxonomic groups are here.

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This is great thank you ! I think though that Uniprot is biaised toward model organisms but for pre-tests it is more than enough.