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. 2023 Dec 21;10:926. doi: 10.1038/s41597-023-02842-4

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© The Author(s) 2023

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — Schematic of case study 1 and 2 use of MarFERReT for annotation of environmental metatranscriptomes. Example workflow showing how MarFERReT data products can be used to annotate unknown assembled sequences and assess taxonomic bins. Boxes indicate datasets; box borders indicate environmental contig sequence data (dashed line), taxonomic and functional annotation from external resources (dotted lines), MarFERReT data products (double lines) and taxonomic and functional annotation results (bold lines). The red diamond indicates a user-constructed DIAMOND³⁰⁶ database for lowest common ancestor determination; prior to this step the user could combine MarFERReT with other libraries for expanded taxonomic coverage as shown in case study 1. Arrows represent processes: (1) construction of DIAMOND³⁰⁶ database using MarFERReT proteins and data, and taxonomy files from NCBI Taxonomy; matching PR² Taxonomy^294,295 identifiers and classifications are also provided in the metadata for alternative classification approaches. (2) Taxonomic annotation of environmental contigs using a DIAMOND³⁰⁶ database built from MarFERReT proteins; (3) Functional annotation of environmental contigs with HMMER³⁰² 3.3 on Pfam²⁹² protein family hmm profiles; (4) Completeness assessment of taxonomically- and functionally-annotated metatranscriptome bins using MarFERReT core transcribed genes.