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Statistical approaches to detecting and analyzing tandem repeats in genomic sequences.

Anisimova M, Pečerska J, Schaper E - Front Bioeng Biotechnol (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Applied Simulation, School of Life Sciences and Facility Management, Zürich University of Applied Sciences (ZHAW) , Wädenswil , Switzerland.

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.

No MeSH data available.


Related in: MedlinePlus

Overview of a generic TR annotation workflow.
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Related In: Results  -  Collection

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Figure 2: Overview of a generic TR annotation workflow.

Mentions: A plausible TR annotation pipeline in three steps could be (1) identify a putative TR unit seed motif; (2) detect all tandem occurrences of this motif in the sequence, forming a putative TR; and (3) for each putative TR validate its statistical significance and filter out redundant predictions. We describe this TR annotation workflow in Figure 2; all functionalities are implemented in TRAL (http://elkeschaper.github.io/tral/).


Statistical approaches to detecting and analyzing tandem repeats in genomic sequences.

Anisimova M, Pečerska J, Schaper E - Front Bioeng Biotechnol (2015)

Overview of a generic TR annotation workflow.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4362331&req=5

Figure 2: Overview of a generic TR annotation workflow.
Mentions: A plausible TR annotation pipeline in three steps could be (1) identify a putative TR unit seed motif; (2) detect all tandem occurrences of this motif in the sequence, forming a putative TR; and (3) for each putative TR validate its statistical significance and filter out redundant predictions. We describe this TR annotation workflow in Figure 2; all functionalities are implemented in TRAL (http://elkeschaper.github.io/tral/).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Applied Simulation, School of Life Sciences and Facility Management, Zürich University of Applied Sciences (ZHAW) , Wädenswil , Switzerland.

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.

No MeSH data available.


Related in: MedlinePlus