Asian Research Thesis Index

Abstract

Simulated alignments are an alternative of benchmark alignments used to comparing the Multiple Sequence Alignments tools. The true evolutionary history of simulated sequence is most important motivation which is very valuable to generate accurate phylogenetic trees and alignments. Simulated alignments are also used to validate and investigate accuracy of multiple sequence alignments methods. The researcher can generate simulated alignments including varying sequence length, indel size, insertion rate, deletion rate and number of sequences. User may have to reconstruct the large number of simulated alignments using simulated tools which is very cumbersome and time consuming job. It is also required professional training and expertise for generation of such a big data. Currently there is no databank available which may help the researcher to download simulated alignments for their study. Major focus of our study is to develop database of simulated alignments (SAliBASE) with varying parameters including varying insertion rate, varying deletion rate, varying sequence length, varying number of sequences and varying number of indel size. For generation of sequence/alignments specifically we generate a collection of trees and use each as a guided tree in the alignments algorithm. For such big data analysis we will use R software that contains various types of packages (ape, base, boot, class, treesim etc.). We use package Treesim for the generating of phylogenetic Tree. Phylogenetic trees are used to describe the relationship among species and genes. Five types of parameters trees we generated using R in Newick format, which is the standard input tree format for simulated tools. We proposed indel-seq-gen simulated tool for generation of simulated alignments and sequences. As a part of this study comparative study of simulated alignments tools will also be conducted.

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