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. 2024 Jan 31;15:936. doi: 10.1038/s41467-024-45024-5

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a A quick database search with the query proteins is performed against a taxonomy-aware reference database. The circles represent individual proteins whose color correspond to different taxonomic lineages: green=metazoa, blue=fungi, purple=bacteria, orange=viridiplantae. The expected lineage one of the query genome (metazoa) is shown as a dotted green frame. Each colored frame with a group of colored dots and a thumbnail image represents one of the many reference genomes in the database. b The bar charts, illustrating cases 1-4, show query versus reference database alignment scores ranked in decreasing order. Taxon information of the best hit is assigned to each query protein together with a confidence score (proportional to dot size). Protein-wise taxon call examples: Case 1: many hits support the metazoa (green) taxon label that is assigned with a high confidence score. Case 2: bacteria (purple) taxon label is assigned but due to limited support, the confidence score is lower. Case 3: Fungi label (blue) from a single hit is assigned albeit with a very low confidence score. Case 4: No hit observed for query in the reference database. c Protein taxon votes are summarized over contigs / scaffolds (∑ sign) and turned into consensus contig calls based on the user-defined threshold. When the consensus taxon label of a contig / scaffold disagrees with that of the query genome, the contig is removed, together with all associated proteins.