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Publication type: Article in scientific journal
Type of review: Peer review (publication)
Title: Statistical approaches to detecting and analyzing tandem repeats in genomic sequences
Authors: Anisimova, Maria
Pečerska, Jūlija
Schaper, Elke
DOI: 10.21256/zhaw-3883
Published in: Frontiers in Bioengineering and Biotechnology
Volume(Issue): 3
Issue: 31
Issue Date: 2015
Publisher / Ed. Institution: Frontiers Research Foundation
ISSN: 2296-4185
Language: English
Subjects: Molecular evolution; Protein domain; Sequence profile model; Tandem repeat annotation; Tandem repeat
Subject (DDC): 004: Computer science
572: Biochemistry
Abstract: Tandem repeats (TRs) are frequently observed in genomes across all domains of life. Evidence suggests that some TRs are crucial for proteins with fundamental biological functions and can be associated with virulence, resistance, and infectious/neurodegenerative diseases. Genome-scale systematic studies of TRs have the potential to unveil core mechanisms governing TR evolution and TR roles in shaping genomes. However, TR-related studies are often non-trivial due to heterogeneous and sometimes fast evolving TR regions. In this review, we discuss these intricacies and their consequences. We present our recent contributions to computational and statistical approaches for TR significance testing, sequence profile-based TR annotation, TR-aware sequence alignment, phylogenetic analyses of TR unit number and order, and TR benchmarks. Importantly, all these methods explicitly rely on the evolutionary definition of a tandem repeat as a sequence of adjacent repeat units stemming from a common ancestor. The discussed work has a focus on protein TRs, yet is generally applicable to nucleic acid TRs, sharing similar features.
Fulltext version: Published version
License (according to publishing contract): CC BY 4.0: Attribution 4.0 International
Departement: Life Sciences and Facility Management
Organisational Unit: Institute of Computational Life Sciences (ICLS)
Appears in collections:Publikationen Life Sciences und Facility Management

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