A System for Phylogenetic Analyses over Alignments of Next Generation Sequence Data

Abstract

A large quantity of DNA sequence data is being generated at high speed and in low cost by next generation sequencing (NGS) technology in recent years. NGS influences wide range of biology, including evolutionary biology, which is the field that infers the evolutionary relationships of genes or organisms from sequence data. In particular, the phylogenetic analyses using massive amount of data generated by NGS have been actively conducted. To infer the phylogenetic relationship, a number of alignments that comprise sets of sequences need to be maintained, i.e., they need to be updated whenever new sequence data become available. However, there have been no database that support updates of alignments, i.e., addition and/or removal of sequences from existing alignments. Instead, individual researchers independently update their alignments manually. To cope with this problem, we propose a system for phylogenetic analyses over alignments of NGS data. It takes as input NGS data, predicts the orthologue that each sequence belongs to, and updates the alignments. Moreover, by describing the related alignments in tree structure, it can maintain stored alignments in a systematic way. To prove the concept, we implement a prototype web application. We expect that our system help biological researchers carry out phylogenetic analysis on large scale data including those from NGS).