SPAI: an interactive platform for indel analysis.

Mohammad Shabbir Hasan,Liqing Zhang

doi:10.1186/s12864-016-2824-x

Abstract

BackgroundInsertions and Deletions (Indels) are the most common form of structural variation in human genome. Indels not only contribute to genetic diversity but also cause diseases. Therefore assessing indels in human genome has become an interesting topic to the research community. This increasing interest on indel calling research has resulted into the development of a good number of indel calling tools. However, all of these tools are command line based and require expertise from Computer Science (CS) to execute them which makes it challenging for researchers from non-CS background.MethodsIn this paper, we describe an interactive platform named SPAI which stands for Single Platform for Analyzing Indels.ResultsBeing a Graphical User Interface (GUI) tool, SPAI facilitates users to run several popular indel calling tools and perform several analyses on the indel calling results without knowing any command line programming.ConclusionsSPAI is written in Java and tested in Linux operating system.

Highlights

Insertions and Deletions (Indels) are the most common form of structural variation in human genome
In this paper we addressed two research questions that are given below: What is the necessity of creating a Graphical User Interface (GUI) for existing indel calling tools? Researchers heavily depend on existing command line programs for calling indels from their dataset as well as for downstream analysis to the problems of their research domain
The research question that we addressed is how SPAI can help in this context? SPAI comes with a list of known indels [42] for human genome which has been used as benchmark dataset by many researchers

Summary

Introduction

Insertions and Deletions (Indels) are the most common form of structural variation in human genome. Assessing indels in human genome has become an interesting topic to the research community. This increasing interest on indel calling research has resulted into the development of a good number of indel calling tools. All of these tools are command line based and require expertise from Computer Science (CS) to execute them which makes it challenging for researchers from non-CS background. Cystic Fibrosis, one of the most common genetic diseases in humans, is caused due to the deletion of 3 base pairs (bps) which leads to the elimination of a single amino acid from the encoded protein [5]. In addition to causing diseases, indels within the promoter region influence gene expression and can be used to explain the difference in gene expression observed in different human [13] which apparently brings the use of indels as genetic markers in natural population [14]

Methods

Results

Conclusion