Please use this identifier to cite or link to this item: http://hdl.handle.net/10773/25204
Title: A Dawson-like clustering of human mitochondrial DNA sequences based on protein coding region
Author: Soares, Inês
Duarte, Rui
Guedes de Oliveira, António
Amorim, António
Keywords: Mitochondrial DNA
Genome comparison
Sequence alignment
Protein coding region
Haplogroup assignment
Dawson construction
Issue Date: 2019
Publisher: Elsevier
Abstract: In the present paper, our main goal is focused in developing fast algorithms for human mtDNA sequence analyses, requiring minimum and explicit assumptions on mutation models and evolutionary pathways. We propose a new approach based on a construction of Dawson, a technique based on the ordering of the variable sites. In this approach, the first step corresponds to the computation of the order of the positions according to their capacity to separate the sequences into dichotomous groups. Aiming to avoid or at least to minimize the consideration of ambiguous evolutionary events such as insertions/deletions and recurrence, which cause well-known alignment problems, in the present study we only work with the protein coding sequence, the clearly more stable region in human mitochondrial genomes. This method was tested in a small set of 99 human mtDNA comprising representatives of all major haplogroups. The developed approach showed to be a choice to automate the clustering of human mtDNA sequences into broad groups, the output being in agreement with the canonical classification into macro-haplogroups deposited in the Phylotree database.
Peer review: yes
URI: http://hdl.handle.net/10773/25204
DOI: 10.1016/j.dam.2018.12.021
ISSN: 0166-218X
Appears in Collections:CIDMA - Artigos
AGG - Artigos

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