Assessing the many aspects of protein-coding gene annotation quality with OMArk

Dataset associated to the OMArk paper.

Contain four archives:

SuppTables

The Supplementary Table files referred to in the paper

OMAmerDB:

The OMAmer database constructed using the whole dataset of the OMA database (December 2021 Release) and used in the paper. An OMAmer database is necessary to run OMArk.

Simulation:
Proteomes with artificially introduced errors, contaminants or depleted completeness, used to assess OMArk's performance. The archive contains the generated proteomes (Simulated_Data*) and their OMArk quality assessments (OMArk_Results). They also contains the OMAmer results (OMAmer_Placements) that were used to run OMArk and BUSCO completeness assessments (BUSCO_Results).

*Note that for storage efficiency, only the non-redundant part of the data (added errors, added contamination, random fraction of proteomes) are stored there. The full modified proteome can be regenerated from these data and the source proteomes.

Reference Proteomes:

The UniProt Reference Proteomes (Proteomes) (2021_04) and their proteome quality assesment results according to OMArk. The archive also contains the OMAmer results (OMAmerResults) that were used to run OMArk (OMArk_Results), and BUSCO completeness assesments (BUSCO_Results).