Open Reading Frame Phylogenetic Analysis on the Cloud

Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus. 1. Introduction Understanding the evolutionary relationships between groups of organisms has become increasingly reliant on phylogenetic analysis. Phylogenies are usually presented as tree diagrams, known as phylogenetic trees. These trees are constructed from genetic similarities and differences between different organisms. Comparative sequence analysis is a useful method by which one can identify gene, infer the function of a gene's product, and identify novel functional elements. By comparing several sequences along their entire length, researchers can find conserved residues that are likely preserved by natural selection. Reconstructing ancestral sequences can reveal the timing and directionality of mutations. These comparative analyses rely on the phylogenetic tree construct. A reading frame is a set of consecutive, nonoverlapping triplets of three consecutive nucleotides. A codon is a triplet equating to an amino acid or stop signal during translation. An open reading frame (ORF) is the section of reading frame containing no stop codons. A protein cannot be made if RNA transcription ceases prior to reaching the stop codon. Therefore, to ensure that the stop codon is translated at the correct position, the transcription termination pause site is located after the ORF. The ORFs can identify translated regions in DNA sequences. Long ORFs indicate candidate protein coding regions in a DNA sequence. ORFs also have been utilized to classify various virus families [1–3], including members of Norovirus [3, 4]. The Open Reading