Inferring Phylogenies from Physico-Chemical Properties of DNA

Abstract

Phylogenetic analysis relies on alignment of related sequences from different species to obtain the distances between these species. The quality of the alignment and the distance measure would depend on the alignment parameters that are used. In this work, we propose to use Relative Complexity Measure (RCM) method to find the distances between the sequences which is a parameter independent measure. We used DNA sequences from Candida species and phylogenetic trees were obtained using un-weighted pair-group with arithmetic mean method. We used three reduced alphabets for the DNA sequences which were clustered by taking into account different physico-chemical properties of DNA. RCM gives as good results as the distance determination method and among the physico-chemical properties, Keto/Amino grouping is found to give the most accurate tree which is topologically closest to the desired phylogeny.

New Perspectives on Reverse Translation: Brief History and Updates

“…Some amino acids are formed with simple molecules (e.g., a single hydrogen in glycine) while others are more complex in their structure (e.g., ring structures in phenylalanine, tryptophan, and tyrosine) [44]. In comparison, there are only two groups of nucleobases in nucleotides: those with a single-ringed pyrimidine (i.e., thymine (T), U, and C) and those with a double-ringed purine (i.e., adenine (A) and guanine (G)) [45]. These monomeric variation di昀昀erences make the probing of molecules required for informational transfer di昀케cult.…”