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REP2: A Web Server to Detect Common Tandem Repeats in Protein Sequences.
Mohamed Kamel1, Kristina Kastano2, Pablo Mier2
1Department of Computer Science, Faculty of Mathematics and Informatics, University of M'sila, 28000 M'sila, Algeria; Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany.
Journal of Molecular Biology
|May 11, 2021
Summary
Tandem repeats (TRs) in proteins are crucial for interactions but hard to detect. The new REP2 web server improves TR analysis in sequences, aiding evolutionary studies.
Area of Science:
- Protein sequence analysis
- Bioinformatics
- Computational biology
Background:
- Tandem repeats (TRs) in protein sequences rapidly form domains essential for protein interactions.
- The rapid divergence of TRs challenges accurate detection using traditional sequence comparison methods.
- Predicting TRs is advantageous due to their structural roles and frequency in proteomes.
Purpose of the Study:
- To introduce REP2, a novel web server for analyzing tandem repeats in protein sequences.
- To enhance the detection and analysis capabilities for TRs in individual and aligned sequences.
- To provide precomputed TR analyses for a large set of proteomes for comparative genomics.
Main Methods:
- Development of the REP2 web server for TR analysis.
- Utilizing curated profiles and thresholds for TR detection.
- Precomputing analyses for 78 UniProt reference proteomes.
Main Results:
- REP2 enables comprehensive analysis of TRs in protein sequences.
- Precomputed data for 78 proteomes are available for download and analysis.
- The server facilitates the study of TR evolution through comparative genomics.
Conclusions:
- The REP2 web server offers an improved method for detecting and analyzing tandem repeats in protein sequences.
- REP2 supports evolutionary studies of TRs by providing accessible, precomputed proteomic data.
- This tool aids researchers in understanding the role and evolution of TRs in protein structure and function.
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