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dereplicate proteins on genus level to reduce database size #21

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jvollme opened this issue Feb 21, 2022 · 0 comments
Open

dereplicate proteins on genus level to reduce database size #21

jvollme opened this issue Feb 21, 2022 · 0 comments
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jvollme commented Feb 21, 2022

maybe use 98% aminoacid identity cut-off?
proteins that are unique for one species in a genus would still be attributed to that individual species (but only one copy would be kept, in case of multi-copy entries)
"redundant" proteins, that occur identically in multiple species of a genus would be attributed to the genus instead of the species (again only represented by one copy)
--> reduces dataset size
--> increases diamond/blast search speeds
--> increases speed of LCA-classifications (a little bit)?

@jvollme jvollme added this to the improvementsB milestone Feb 21, 2022
@jvollme jvollme self-assigned this Feb 21, 2022
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