bioinformatics solution towards understanding the ...

Demos: General neuroinformatics

D12 GenomeVX: bioinformatics solution towards understanding the genome-wide comparative analyses of different human populations Zeeshan Ahmed1,2,3,4,*, Saman Zeeshan2,3, Nicolai Peschel4, Thomas Dandekar3 1. The Jackson Laboratory for Genomic Medicine, USA 2. School of Medicine, University of Massachusetts, USA 3. Department of Bioinformatics, Biocenter, University of Wuerzburg, Germany 4. Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Germany We have proposed a new computational, Bioinformatics solution i.e. GenomeVX, towards the field of Genomics and Nucleic acid research. GenomeVX helps in understanding the Genome-wide comparative analyses of different human populations, as well as between species, focusing on the association studies relating genetic variation to disease with evidence of mutations. GenomeVX extracts data from the fields in VCF file [generated by the 1000 Genome Browser (1)] and displays alleles for the substitutions and variations (SNP). The graphical interface of the GenomeVX is very simple to install and use. It is a desktop application which offers two integrated modules: VCF File Editor and VCF Extracted and Converted Information. Using these modules, user can load the VCF files in to the GenomeVX and can extract, parse and convert the nucleotides’ complex respective numbers to the representative notations (e.g., ACTG). Furthermore, it helps the user to convert analysed data in to the Microsoft Excel Sheets for better analysis, statistical visualization and sharing. The overall workflow and wiring of the components of the GenomeVX is presented in Figure 1. GenomeVX implementation follows the principles of our newly proposed software engineering paradigm i.e. Butterfly (2, 3). It is programmed in C# programming language, using Microsoft Visual Studio Dot Net Framework and only compatible to the Microsoft Windows Operating Systems (preferred OS version: 7). Most recent available version of the GenomeVX is in testing and in limited use, and we are focusing on the future research and development objectives by enhancing the its capabilities with more features. The six steps installation process of GenomeVX is presented in the Figure 2 and it is freely available for any non-commercial, academic and scientific use at the following web link: (https://zenodo.org/record/13815?ln=en#.VOZSxC6ZNS0). Keywords: Bioinformatics software, GenomeVX; Genome 1000 Browser, Genomics, Nucleic acid research Acknowledgements The authors would like to thank German Research Foundation (DFG SFB 1047 and TR34/Z1) for funding on this research. The authors thank to the University of Wuerzburg Germany, University of Massachusetts USA and The Jackson Laboratory USA for support in this

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Figure 1. GenomeVX’ components and workflow. The Figure 1 shows extracting of data from 1000 Genome Brower, wiring of components of the GenomeVX and conversion of output into the Microsoft Excel format.

Figure 2. GenomeVX installation process. The Figure 2 presents six steps installation process of the GenomeVX.

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publication. Authors also thank to all interested colleagues for critical input on the approach and anonymous reviewers for helpful comments. Conflict of Interest The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. References 1. 1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, et al. A map of human genome variation from population-scale sequencing. Nature (2010) 467(7319):1061–73. doi: 10.1038/nature09534 PMID:NOPMID 2. Ahmed Z, Saman Z, Dandekar T. Developing sustainable software solutions for bioinformatics by the ‘Butterfly’ paradigm. F1000Research (2014). doi: 10.12688/f1000research.3681.2 PMID:25383181 3. Ahmed Z, Zeeshan S. Cultivating software solutions development in the scientific academia. Recent Pat Comput Sci (2014) 7(1):54–66. doi: 10.2174/2213275907666140612 210552 PMID:NOPMID

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