Related Experiment Video
Updated: Jul 23, 2025

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
Published on: November 17, 2019
StandEnA: a customizable workflow for standardized annotation and generating a presence-absence matrix of proteins
Fatma Chafra1,2, Felipe Borim Correa1,3, Faith Oni1,3
1Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany.
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.
More Related Videos
09:52A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease
Published on: January 10, 2025
05:37Label-Free Quantitative Proteomics Workflow for Discovery-Driven Host-Pathogen Interactions
Published on: October 20, 2020
Related Concept Videos
Genome Annotation and Assembly
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Tagging and Fusion Proteins
Protein Organization
Protein Complex Assembly
Proteomics
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...