AI Article Synopsis
- Genome annotation tools help standardize outputs but limit user customization, which affects their flexibility in further analysis.
- StandEnA is a new command-line tool for Linux that allows users to create custom databases by pulling protein sequences from various sources, using a defined list of standard names.
- StandEnA is open-source and can be accessed online, with supplementary data available for further research.
Article Abstract
Motivation: Several genome annotation tools standardize annotation outputs for comparability. During standardization, these tools do not allow user-friendly customization of annotation databases; limiting their flexibility and applicability in downstream analysis.
Results: StandEnA is a user-friendly command-line tool for Linux that facilitates the generation of custom databases by retrieving protein sequences from multiple databases. Directed by a user-defined list of standard names, StandEnA retrieves synonyms to search for corresponding sequences in a set of public databases. Custom databases are used in prokaryotic genome annotation to generate standardized presence-absence matrices and reference files containing standard database identifiers. To showcase StandEnA, we applied it to six metagenome-assembled genomes to analyze three different pathways.
Availability And Implementation: StandEnA is an open-source software available at https://github.com/mdsufz/StandEnA.
Supplementary Information: Supplementary data are available at online.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10336186 | PMC |
| http://dx.doi.org/10.1093/bioadv/vbad069 | DOI Listing |
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