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Updated: Sep 11, 2025
09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
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Arche: An Advanced Flexible Tool for High-Throughput Annotation of Functions on Microbial Contigs
IEEE Transactions on Computational Biology and Bioinformatics
|August 14, 2025
Summary
Arche is a new command-line tool for microbial genome annotation. It offers a flexible workflow combining multiple search strategies and databases, improving functional identifier retrieval for genomic and metagenomic studies.
Area of Science:
- Genomics
- Bioinformatics
- Microbial genomics
Background:
- Increasing microbial genomic data necessitates advanced annotation tools.
- Existing pipelines face limitations in database integration, installation complexity, and computational demands.
Purpose of the Study:
- To introduce Arche, a command-line annotation pipeline designed for comprehensive and accessible microbial genome annotation.
- To address limitations of current tools by offering a flexible and integrated workflow.
Main Methods:
- Arche integrates multiple search strategies (BLAST, DIAMOND, HMMER3) and databases (UniProtKB, KOfam, TIGRFAMs, NCBIFAMs, Pfam).
- It supports annotation of prokaryotic genomes and metagenomes.
- Functional tables include enzyme commission (E.C.) numbers, KEGG and eggNOG identifiers, gene names, and protein descriptions.
Main Results:
- Arche demonstrates superior retrieval of functional identifiers per gene compared to tools like Prokka, Bakta, and RAST.
- Benchmarking confirms its effectiveness in annotating prokaryotic genomes and metagenomes.
Conclusions:
- Arche provides a practical and robust solution for functional annotation.
- Its modularity, compatibility with standard systems, and manageable database requirements make it a valuable tool for genomic and metagenomic studies.
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