LifePrint: a novel k-tuple distance method for construction of phylogenetic trees
Authors Reyes-Prieto F, Garcia-Chequer, Jaimes-Díaz, Casique-Almazan J, Espinosa-Lara JM, Palma-Orozco R, Mendez Tenorio A, Maldonado-Rodríguez R, Beattie K
Published 20 January 2011 Volume 2011:4 Pages 13—27
Review by Single anonymous peer review
Peer reviewer comments 2
Fabián Reyes-Prieto1, Adda J García-Chéquer1, Hueman Jaimes-Díaz1, Janet Casique-Almazán1, Juana M Espinosa-Lara1, Rosaura Palma-Orozco2, Alfonso Méndez-Tenorio1, Rogelio Maldonado-Rodríguez1, Kenneth L Beattie3
1Laboratory of Biotechnology and Genomic Bioinformatics, Department of Biochemistry, National School of Biological Sciences, 2Superior School of Computer Sciences, National Polytechnic Institute, Mexico City, Mexico; 3Amerigenics Inc, Crossville, Tennessee, USA
Purpose: Here we describe LifePrint, a sequence alignment-independent k-tuple distance method to estimate relatedness between complete genomes.
Methods: We designed a representative sample of all possible DNA tuples of length 9 (9-tuples). The final sample comprises 1878 tuples (called the LifePrint set of 9-tuples; LPS9) that are distinct from each other by at least two internal and noncontiguous nucleotide differences. For validation of our k-tuple distance method, we analyzed several real and simulated viroid genomes. Using different distance metrics, we scrutinized diverse viroid genomes to estimate the k-tuple distances between these genomic sequences. Then we used the estimated genomic k-tuple distances to construct phylogenetic trees using the neighbor-joining algorithm. A comparison of the accuracy of LPS9 and the previously reported 5-tuple method was made using symmetric differences between the trees estimated from each method and a simulated “true” phylogenetic tree.
Results: The identified optimal search scheme for LPS9 allows only up to two nucleotide differences between each 9-tuple and the scrutinized genome. Similarity search results of simulated viroid genomes indicate that, in most cases, LPS9 is able to detect single-base substitutions between genomes efficiently. Analysis of simulated genomic variants with a high proportion of base substitutions indicates that LPS9 is able to discern relationships between genomic variants with up to 40% of nucleotide substitution.
Conclusion: Our LPS9 method generates more accurate phylogenetic reconstructions than the previously proposed 5-tuples strategy. LPS9-reconstructed trees show higher bootstrap proportion values than distance trees derived from the 5-tuple method.
Keywords: phylogeny, sequence alignment, similarity search, tuple, viroid
This work is published and licensed by Dove Medical Press Limited. The full terms of this license are available at https://www.dovepress.com/terms.php and incorporate the Creative Commons Attribution - Non Commercial (unported, v3.0) License. By accessing the work you hereby accept the Terms. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. For permission for commercial use of this work, please see paragraphs 4.2 and 5 of our Terms.Download Article [PDF] View Full Text [HTML][Machine readable]