Discovery Of Evolutionary Patterns In Ribosomal Rna Data Using Markov Models

The paper deals with the construction of the phylogenetic tree and multiple sequence alignment of ribosomal RNA datasets downloaded from Silva comprehensive rRNA database using markov models. The new method is based on the concept of comparing the similarity/dissimilarity between two Markov models using Kullback-Leibler divergence for construction of pair-wise distance matrix. The alignment accuracy (sum of pair's scores) of the multiple sequence alignment of these datasets is compared with ClustalX software (progressive alignment). The statistical significance and the deviation of the alignment accuracy from ClustalX software was found by analysis of variance (ANOVA). Our results using the new method showed good agreement with the ClustalX-Multiple Sequence Alignment and phylogenetic tree and confirming the use of probabilistic Markov models in rRNA dataset analysis. All datasets and computer codes written in MATLAB are available upon request from the first author (somashekar mt@ hotmail. com).