%0 Journal Article
%T LifePrint: a novel k-tuple distance method for construction of phylogenetic trees
%A Fabi&aacute
%A n Reyes-Prieto
%A Adda J Garc&iacute
%A a-Ch&eacute
%A quer
%A Hueman Jaimes-D&iacute
%A az
%A et al
%J Advances and Applications in Bioinformatics and Chemistry
%D 2011
%I Dove Medical Press
%X Fabi¨¢n Reyes-Prieto1, Adda J Garc¨ªa-Ch¨¦quer1, Hueman Jaimes-D¨ªaz1, Janet Casique-Almaz¨¢n1, Juana M Espinosa-Lara1, Rosaura Palma-Orozco2, Alfonso M¨¦ndez-Tenorio1, Rogelio Maldonado-Rodr¨ªguez1, Kenneth L Beattie31Laboratory 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, USAPurpose: 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
%U http://www.dovepress.com/lifeprint-a-novel-k-tuple-distance-method-for-construction-of-phylogen-a6102