StandEnA: a customizable workflow for standardized annotation and generating a presence–absence matrix of proteins-Reference-Cited by-同舟云学术

StandEnA: a customizable workflow for standardized annotation and generating a presence–absence matrix of proteins

Published:2023-01-01 Issue:1 Volume:3 Page:
ISSN:2635-0041
Container-title:Bioinformatics Advances
language:en
Short-container-title:

Author:

Chafra Fatma¹²,Borim Correa Felipe¹³,Oni Faith¹³,Konu Karakayalı Özlen²⁴⁵,Stadler Peter F³⁶⁷⁸⁹¹⁰^ORCID,Nunes da Rocha Ulisses¹³^ORCID

Affiliation:

1. Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ , Leipzig 04318, Germany

2. Department of Molecular Biology and Genetics, Bilkent University , Ankara 06800, Turkey

3. Department of Computer Science and Interdisciplinary Center of Bioinformatics, University of Leipzig , Leipzig 04107, Germany

4. Interdisciplinary Program in Neuroscience, Bilkent University , Ankara 06800, Turkey

5. UNAM-Institute of Materials Science and Nanotechnology, Bilkent University , Ankara 06800, Turkey

6. Interdisciplinary Center for Bioinformatics, German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, Leipzig Research Center for Civilization Diseases, Leipzig Research Center for Civilization Diseases (LIFE), University of Leipzig , Leipzig 04109, Germany

7. Max Planck Institute for Mathematics in the Sciences , Leipzig 04103, Germany

8. Institute for Theoretical Chemistry, University of Vienna , Vienna 1090, Austria

9. Facultad de Ciencias, Universidad National de Colombia , Sede Bogotá 111711, Colombia

10. Santa Fe Institute , Santa Fe, NM 87501, USA

Abstract

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 Bioinformatics Advances online.

Funder

Deutsche Forschungsgemeinschaft

German Research Foundation

Publisher

Oxford University Press (OUP)

Subject

Computer Science Applications,Genetics,Molecular Biology,Structural Biology

Link

https://academic.oup.com/bioinformaticsadvances/advance-article-pdf/doi/10.1093/bioadv/vbad069/50563052/vbad069.pdf

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