A time warping approach to multiple sequence alignment Articles uri icon

publication date

  • April 2017

start page

  • 133

end page

  • 144

issue

  • 2

volume

  • 16

international standard serial number (ISSN)

  • 2194-6302

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.

keywords

  • alignment; dynamic time warping; multiple sequence alignment; warping