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Related Concept Videos

The Evidence for Evolution02:55

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John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
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Progressive multiple sequence alignment with indel evolution.

Massimo Maiolo1,2,3, Xiaolei Zhang4, Manuel Gil1,3

  • 1Institute of Applied Simulation, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Grüentalstrasse 14, P.O. Box, Waedenswil, CH-8820, Switzerland.

BMC Bioinformatics
|September 23, 2018
PubMed
Summary
This summary is machine-generated.

This study introduces a new multiple sequence alignment (MSA) method that rigorously models indel evolution on phylogenies. The approach provides phylogenetically meaningful gap patterns, improving upon existing heuristics for genomic analysis.

Keywords:
Dynamic programmingIndelPhylogenyPoisson processSequence alignment

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Area of Science:

  • Genomics
  • Computational Biology
  • Bioinformatics

Background:

  • Multiple sequence alignment (MSA) is vital in genomics but computationally challenging (NP-hard).
  • Current MSA methods use progressive heuristics and Markov models for character substitutions, but lack explicit indel evolution modeling.
  • Failure to model indel dynamics can result in inaccurate alignments inconsistent with phylogenetic relationships.

Purpose of the Study:

  • To develop a novel dynamic programming algorithm for multiple sequence alignment (MSA) that rigorously models indel evolution.
  • To implement a progressive alignment strategy guided by a phylogeny using a new maximum likelihood approach.

Main Methods:

  • Developed a dynamic programming algorithm to align two MSAs (represented by homology paths) under the Poisson Indel Process (PIP) model in polynomial time.
  • Applied the algorithm progressively along a guide tree for multiple sequence alignment.
  • Validated the method through simulations and comparison with existing methods on real genomic data.

Main Results:

  • The new method achieves polynomial time complexity for progressive alignment with explicit indel evolution modeling.
  • It generates phylogenetically meaningful gap patterns, comparable to popular methods like PRANK.
  • The inferred gap patterns align with qualitative predictions from prior research.

Conclusions:

  • This work presents the first polynomial-time progressive aligner with a rigorous mathematical formulation for indel evolution.
  • The method offers an alternative to existing tools, producing biologically relevant alignments.
  • The algorithm is publicly available as a C++ program (ProPIP).