SNP-E: A New Method For Multiple Sequence Alignments Analysis And Accurate Single Nucleotide Polymorphism Evaluation

Melody N Hemmati-Sholeh,Larry A Sholeh,David A Lightfoot

doi:10.5147/ajb.v3i1.31

Abstract

Identification of single nucleotide polymorphisms (SNPs) and insertion-deletion mutations are important for discovering the connection between the genetic mutations and complex diseases. The objective of this study was to develop a sensitive and accurate computational method for SNP detection among Multiple Sequence Alignments (MSAs) to be run on Microsoft Office SuiteTM and WindowsTM. The SNP-Evaluator, was designed to simulate the process of human eye visual change-identification. Analysis of three 82-Kbp genomic loci derived from Sanger sequencing and the corresponding SNPs from 31 genomes from IlluminaTM sequencing of soybean (Glycine max L. Merr.) demonstrated that the SNP-E was an effective method for medium-scale genomic research.

Highlights

Identification of single nucleotide polymorphisms (SNPs) and insertion-deletion mutations are important for discovering the connection between the genetic mutations and complex diseases
Single Nucleotide Polymorphism (SNP) and mutations among highly polymorphic regions are often associated with useful traits such as resistance to disease (Ruben et al, 2006; Srour et al, 2012) and identification of them is important to discover the link between the genetic mutations and complex diseases (Zhang et al, 2005)
Manual annotation was needed for SNP evaluation at any stage of process

Summary

Introduction

Identification of single nucleotide polymorphisms (SNPs) and insertion-deletion mutations are important for discovering the connection between the genetic mutations and complex diseases. It is capable of making a confident identification (base-call) because visual confirmation is not a reliable option for sequences from generation sequencer with higher number of sequences at the cost of higher error rates and patchy sequence coverage This method needed to give the young researchers who are still enhancing their skills in different programming languages and would like to work with medium-scale genomic sequences, more flexibility for generation data analysis. By applying this method, researchers have the ability to associate a specific alignment nucleotide identification number to each nucleotide (nucleotide’s ID), customize data analysis and apply functions and formulas on data (nucleotides) This method functions as a visible tool due to its table format that can provide SNP-E the capability to simulate the process of human eye visual change-identification

Objectives

Methods

Results