A time warping approach to multiple sequence alignment

DOI10.1515/SAGMB-2016-0043MaRDI QIDQ2406175zbMATH OpenOpenAlexWikidataFDO

Authors Ana Arribas-Gil, Catherine Matias

Publication date 27 September 2017

Published in Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1606.06017

zbMATH Keywords

alignmentdynamic time warpingmultiple sequence alignmentwarping

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40)

Abstract: We propose an approach for multiple sequence alignment (MSA) derived from the dynamic time warping viewpoint and recent techniques of curve synchronization developed in the context of functional data analysis. Starting from pairwise alignments of all the sequences (viewed as paths in a certain space), we construct a median path that represents the MSA we are looking for. We establish a proof of concept that our method could be an interesting ingredient to include into refined MSA techniques. We present a simple synthetic experiment as well as the study of a benchmark dataset, together with comparisons with 2 widely used MSA softwares.

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Cites work

• An Overview of Sequence Comparison: Time Warps, String Edits, and Macromolecules
• Biological Sequence Analysis
• Expected time bounds for selection
• Functional Convex Averaging and Synchronization for Time-Warped Random Curves
• Pairwise curve synchronization for functional data
• Pairwise dynamic time warping for event data
• Parameter estimation in multiple-hidden i.i.d. models from biological multiple alignment
• Parameter Estimation in Pair‐hidden Markov Models

Cited in

(5)

• Pairwise dynamic time warping for event data
• Symmetric time warping, Boltzmann pair probabilities and functional genomics
• A time series representation of protein sequences for similarity comparison
• On the alignment of multiple time series fragments
• Summarizing a set of time series by averaging: from Steiner sequence to compact multiple alignment

Describes a project that uses

Uses Software

• ProbCons
• MUSCLE
• Biostrings
• ClustalW
• MAFFT
• T-coffee
• MUMMALS
• Algorithm 489

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