Microeukaryotic Protein Database (VDB_Microeukaryotic_v1)

Version: VDB_Microeukaryotic_v1

Contains 4 files: 

-rw-r--r--  1 jespinoz  staff    10G Apr 18 19:46 reference.rmdup.iupac.relabeled.no_deprecated.complete_lineage.faa.gz

-rw-r--r--  1 jespinoz  staff   167M Apr 18 19:40 target_to_source.dict.pkl.gz

-rw-r--r--  1 jespinoz  staff   605K Apr 18 19:40 source_to_lineage.dict.pkl.gz

-rw-r--r--  1 jespinoz  staff   542K Apr 18 19:42 source_taxonomy.tsv.gz

* The main fasta protein file which is the dereplicated combination of NR (only protista and fungus), MMETSP, EukZoo, and EukProt.  Only complete lineages are included since this is partially used for classification. 

* .pkl.gz are Python gzipped pickled dictionaries. 

* target_to_source.dict.pkl.gz has mapping between identifiers in fasta file and the original source

* source_to_lineage.dict.pkl.gz has the mapping between source identifiers and lineage strings (e.g., c__Aconoidasida;o__Haemosporida;f__Haemoproteidae;g__Haemoproteus;s__Haemoproteus sp. hCWT4)

* source_taxonomy.tsv.gz has the taxonomy for each source identifier

Citation:

* Espinoza, J.L., Dupont, C.L. VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes. BMC Bioinformatics 23, 419 (2022). https://doi.org/10.1186/s12859-022-04973-8

* Espinoza, Josh (2022): Microeukaryotic Protein Database. figshare. Dataset. https://doi.org/10.6084/m9.figshare.19668855.v1