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Taxonomy Analysis in Bacteria Kingdom based onProtein Domain: A Comparison Study

Wang, B.; Zhou, J.; Jin, Y.; Hu, M.; Zhao, Y.; Wang, X.; Yang, H.; Gong, X.; Zhang, F.; Zhang, Z.; Kang, F.; Liang, L.; Yue, J.; Ren, H.

2021-09-20 bioinformatics
10.1101/2021.09.17.460715 bioRxiv
Show abstract

The taxonomy research on the bacterial kingdom is important and can be usually conducted by the analysis on conserved genes, 16s rRNA, protein domain, and so on. Comparatively, the protein domains maintain a most direct relationship with phenotypes. In this paper, based on the protein domain, we propose a 3-step framework to standardize the classification process of bacteria. Different model candidates are involved and discussed in each step. By comparing the classification results with existing taxonomy, we select the most appropriate candidate to improve the framework, and furthermore, discuss their biological significance. Finally, we put forward taxonomy suggestions based on the best classification results. Significance StatementWe standardize a 3-step framework to carry out bacterial taxonomy research based on protein domain. Furthermore, we filter out the best solution in each step that can together generate the most appropriate classification result, and at the same time, we discuss the biological significant it indicates. Finally, we propose suggestions on NCBI bacterial taxonomy based on the classification results.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.