ISSN: 0974-7230
Journal of Computer Science & Systems Biology
Like us on:
Make the best use of Scientific Research and information from our 700+ peer reviewed, Open Access Journals that operates with the help of 50,000+ Editorial Board Members and esteemed reviewers and 1000+ Scientific associations in Medical, Clinical, Pharmaceutical, Engineering, Technology and Management Fields.
 
Meet Inspiring Speakers and Experts at our 3000+ Global Conferenceseries Events with over 600+ Conferences, 1200+ Symposiums and 1200+ Workshops on
Medical, Pharma, Engineering, Science, Technology and Business

Computational Study of Viral Segments Inserted within the Regions of Human Genome

P. Pandarinath*, M. Shashi and A. Appa Rao
Department of Computer Sciences, College of Engineering (A) Andhra University, Visakhapatnam- 530 003, Andhra Pradesh, India
Corresponding Author : Dr. P. Pandarinath
Department of Computer Sciences
College of Engineering (A) Andhra University
Visakhapatnam–530 003
Andhra Pradesh, India
E-mail: sriram310@gmail.com
Received August 25, 2010; Accepted August 28, 2010; Published August 28, 2010
Citation: Pandarinath P, Shashi M, Rao AA (2010) Computational Study of Viral Segments Inserted within the Regions of Human Genome. J Comput Sci Syst Biol 3:074-075. doi:10.4172/jcsb.1000060
Copyright: © 2010 Pandarinath P, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Related article at
DownloadPubmed DownloadScholar Google

Visit for more related articles at Journal of Computer Science & Systems Biology

Abstract

Humans have been carrying unwanted viral gene segments since many years and reports suggests that approximately 3-8% of the human genome has been comprised of viral DNA. In this point of view, various viral sequences were downloaded from NCBI Tax Browser and scanned against complete genome of Homo sapiens for the presence of possible viral inserts in human genome. The results from the computational analysis revealed that dengue virus resulted in viral segments inserted in the intron regions of human genome and exon region insertions were observed with polio and simian enterovirus. The alignments which show > 25-30 residues, 90-100% identities and the sequences located in the exon regions were considered.

Keywords
Viral segments; Homo sapiens; Insertions; Intron; Extron; Computational
Introduction
The human genome is the genetic blue print for all cellular structures and activities of the human body. Genes direct the manufacture of cellular proteins which allow cells to carry out normal mechanisms. Defective or mutated genes can direct the cell to make aberrant proteins which in turn cause diseases. There is a growing public demand for genetic information; a heightening curiosity and bewilderment about one’s own genetic predisposition (Teri, 2001).
Every human contains a significant amount of DNA that is not actually human; and contains dormant fossil viruses that have infiltrated the genome. Estimates range from 3-8% of the human genome as being comprised of sections of viral DNA. During the course of a viral infection, some viruses insert their DNA into the host’s genome (proviruses) and direct the host cellular machinery to make the proteins and genetic material needed to make/assemble more viruses. If this gene insertion takes place in a cell that will become an egg or sperm, the host’s offspring’s will have a copy of the virus in every single cell. These and other parasite, self-replicating pieces of nucleic acids have evolved with us over millions of years after being inserted into the human DNA by the virus that infected our ancestors.
According to Cullen, an ancient family of viruses known as HERV-K (for human endogenous retrovirus K), took up permanent residence in the genetic material of Old World monkeys shortly after they diverged from New World monkeys. The viruses then traveled with their simian and pre-human hosts as these species moved along the evolutionary path that led to Homo sapiens (Jin et al., 1999).
Because of these viral gene insertion events, genetic material from inactive viruses accounts for roughly 3 percent of the human genome. Nearly 30-50 copies of HERV-K exist in the human genome, and that some of the copies appear to be active at a low level in normal testicular and placental tissue (Jin et al., 1999). Earlier Japanese researchers found copies of the Bornavirus N (for nucleoproteins) gene inserted an at least four separate locations in the human genome and clearly provided a fossil record of bornavirus (Tina, 2010).
It has been since decades that many viruses have been infecting vertebrates, humans in particular. Experimental evidence suggests that HIV, Epstein-Barr viral segments were inserted in few regions of the human genome. As there are many infectious viruses such as polio, enterovirus, etc, an attempt has been made to identify the insertions of various viral gene segments in either exon/intron region of human genome. To the best of the knowledge, till date there is no evidence of computational analysis to determine the presence of viral inserts in human genome. Keeping this aspect into consideration, various viral sequences were downloaded from NCBI Tax Browser and scanned against complete genome of Homo sapiens for the presence of any inserted segments.
Material and Methods
The genomic sequences of polio virus, simian entero virus and dengue virus were downloaded from the NCBI Genbank database. Blastn algorithm was used to perform similarity search using default parameters and scanned against the complete genome of Homo sapiens. The option, somewhat similar sequences were selected in order to obtain medium length matches. The program compares the query sequence with the human genome sequence and calculates the statistical significance of matches (Altschul et al., 1990).
Sequence tools are used for basic and advanced analysis of nucleotide and protein sequence. The hydropathy plot was used to find cluster of hydrophobic amino acids, which indicate that the polypeptide in question is a transmembrane protein. Molecular Genetic Evolutionary Analysis (MEGA 4) was readily useful for making phylogenic trees and aligning sequences. Discovery studio software was used to perform sequence comparison and structure visualization. The software compares a query sequence with our own sequence and produces a graphical dot plot using dot plot function and displays maps, sites and enzymes.
Results
Polio virus
The blast result of the polio virus 1 strain sabin nucleotide sequence and the human genome shows that the sequence was present in the exon region of sialidase-4 gene (chromosome 2) sequence of Homo sapiens with a match of 32 residues (Supplementary Figures 1 (a) and 1 (b)). The sequence in fasta format of the sialidase 4 gene (subject sequence region) and human polio virus 1 strain sabin (query sequence region) were aligned using bl2Seq. The encoded amino acid matching for both the sequences i.e., PPQSPTWLLYS was visible in the sequence view of the graphics page (Supplementary Figures 2 (a) and 2 (b)). The result of SEQ tools shows that the codon usage and the GC content of the whole genomic sequence was 3446 (46%) (Supplementary Figure 3). The protein sequence shows the properties and the hydropathy plot i.e., protein length was 522 aa and the molecular weight was 55,351 (Supplementary Figure 4). WebLab Viewer generates and display surfaces and features of sialidase 4 (Supplementary Figure 5). The identical pairs (32), transitional pairs (0) and transversional pairs (2) were also obtained (Supplementary Figures 6 (a) and 6 (b)) using MEGA4 software.
Simian entero virus
The blast result of the simian entero virus nucleotide sequence and the human genome shows that the sequence was present in the exon region of cell division cycle 40 homolog gene (chromosome 6) sequence of Homo sapiens with a match of 34 residues (Supplementary Figure 7) and the match of amino acid coding of both the sequences i.e., DWLKILGDWGC was shown graphically (Supplementary Figure 8). The codon usage and the GC content of the whole genomic sequence was 2930 (44.6%) (Supplementary Figure 9). The length of the protein was 616 aa and the molecular weight was 69,548 (Supplementary Figure 10). The surface properties and features of cell division cycle using 40 homologs were presented (Supplementary Figure 11). The identical pairs (34), transitional pairs (2) and transversional pairs (3) were also obtained (Supplementary Figures 12 (a) and 12 (b)).
Dengue virus
The blast result of the dengue virus nucleotide sequence and the human genome shows that the sequence was present in the exon region of inositol polyphosphate-5-phosphatase A (chromosome 10) sequence and ccctc-binding factor (chromosome 16) sequence of Homo sapiens with a match of 34 and 39 residues, respectively (Supplementary Figures 13 (a) and 13 (b)) but the graphics has not shown the residues in the presence of the exon region, where as it was proved that the residues were present in the intron region (Supplementary Figure 14). The result of SEQ tools shows that the codon usage and the GC content of the whole genomic was 7439 (48.7%) (Supplementary Figure 15).
Conclusions
From computational analysis, it was observed that Dengue virus resulted in viral segments inserted in the intron regions of human genome, however, exon region insertions were observed with polio and simian enterovirus. Nearly 33 nucleotide residue segment (91% identities) of Polio virus 1 strain sabin was found to be inserted in two different exon region of Sialidase-4 gene (chromosome 2) sequence of Homo sapiens. Comparing the genome of simian enterovirus SV6 against human genome resulted in 85% match (40 residues) with cell division cycle 40 homolog gene sequence of chromosome 6. The work indicates that with few computational efforts viral inserts in human genome can be identified and represents that further analysis needs to be carried out to study the influence of such inserts in the structural and functional features of respective genes.
Acknowledgements
The authors are thankful to the management of Sir C R Reddy College of Engineering for their support.
References






Select your language of interest to view the total content in your interested language
 
Share This Article
   
 
   
 
Relevant Topics
Disc Advanced DNA Sequencing
Disc Algorithm
Disc Animal and Tissue Engineering
Disc Applications of Bioinformatics
Disc Artificial Intelligence Studies
Disc Artificial intelligence
Disc Artificial neural networks
Disc Bioinformatics Algorithms
Disc Bioinformatics Databases
Disc Bioinformatics Modeling
Disc Bioinformatics Tools
Disc Biology Engineering
Disc Biostatistics: Current Trends
Disc Cancer Proteomics
Disc Chemistry of Biology
Disc Clinical Proteomics
Disc Cloud Computation
Disc Cluster analysis
Disc Comparative genomics
Disc Comparative proteomics
Disc Computational Chemistry
Disc Computational Sciences
Disc Computational drug design
Disc Computer Science
Disc Current Proteomics
Disc Data Mining Current Research
Disc Data algorithms
Disc Data mining applications in genomics
Disc Data mining applications in proteomics
Disc Data mining in drug discovery
Disc Data mining tools
Disc Data modelling and intellegence
Disc Data warehousing
Disc Ethics in Synthetic Biology
Disc Evolution of social network
Disc Evolutionary Optimisation
Disc Evolutionary algorithm
Disc Evolutionary algorithm in datamining
Disc Evolutionary computation
Disc Evolutionary science
Disc Experimental Physics
Disc Findings on Machine Learning
Disc Gene Synthesis
Disc Genome annotation
Disc Genomic data mining
Disc Genomic data warehousing
Disc Germ cell tumours
Disc Handover
Disc Human Proteome Project Applications
Disc Hybrid soft computing
Disc Industrial Biotechnology
Disc Knowledge modelling
Disc Machine Learninng
Disc Mapping of genomes
Disc Mass Spectrometry in Proteomics
Disc Mathematical Modeling
Disc Mathematics for Computer Science
Disc Meta genomics
Disc Microarray Proteomics
Disc Models of Science
Disc Molecular and Cellular Proteomics
Disc Multi Objective Programming
Disc Neural Network
Disc Ontology Engineering
Disc P4 medicine
Disc Physics Models
Disc Protein Sequence Analysis
Disc Proteogenomics
Disc Proteome Profiling
Disc Proteomic Analysis
Disc Proteomic Biomarkers
Disc Proteomics Clinical Applications
Disc Proteomics Research
Disc Proteomics Science
Disc Proteomics data warehousing
Disc Python for Bioinformatics
Disc Quantitative Proteomics
Disc Robotics Research
Disc Scientific Computing
Disc Simulation Computer Science
Disc Statistical data mining
Disc Studies on Computational Biology
Disc Swarm Robotics
Disc Swarm intelligence
Disc Synthetic Biology
Disc Synthetic Biology medicine
Disc Synthetic Biotechnology
Disc Synthetic Genomics
Disc Synthetic biology drugs
Disc Systems Biology
Disc Technologies in Computer Science
Disc Theoretical Chemistry
Disc Theoretical Computer Science
Disc Theoretical Issues in Ergonomics Science
Disc Theoretical Methods
Disc Theoretical and Applied Science
 
Recommended Journals
Disc Swarm Intelligence and Evolutionary Computation Journal
Disc Computer Engineering & Information Technology
Disc Theoretical and Computational Science
Disc Proteomics & Bioinformatics
Disc Data Mining in Genomics & Proteomics Journal
Disc Current Synthetic and Systems Biology
  View More»
 
Article Tools
Disc Export citation
Disc Share/Blog this article
 
Article usage
  Total views: 11138
  [From(publication date):
July-2010 - Jun 26, 2016]
  Breakdown by view type
  HTML page views : 7411
  PDF downloads :3727
 
 

Post your comment

captcha   Reload  Can't read the image? click here to refresh

 
OMICS International Journals
 
Make the best use of Scientific Research and information from our 700 + peer reviewed, Open Access Journals
 
 
OMICS International Conferences 2016-17
 
Meet Inspiring Speakers and Experts at our 3000+ Global Annual Meetings
 
 

Contact Us

Agri, Food, Aqua and Veterinary Science Journals

Dr. Krish

agrifoodaquavet@omicsinc.com

1-702-714-7001 Extn: 9040

Clinical and Biochemistry Journals

Datta A

clinical_biochem@omicsinc.com

1-702-714-7001Extn: 9037

Business & Management Journals

Ronald

business@omicsinc.com

1-702-714-7001Extn: 9042

Chemical Engineering and Chemistry Journals

Gabriel Shaw

chemicaleng_chemistry@omicsinc.com

1-702-714-7001 Extn: 9040

Earth & Environmental Sciences

Katie Wilson

environmentalsci@omicsinc.com

1-702-714-7001Extn: 9042

Engineering Journals

James Franklin

engineering@omicsinc.com

1-702-714-7001Extn: 9042

General Science and Health care Journals

Andrea Jason

generalsci_healthcare@omicsinc.com

1-702-714-7001Extn: 9043

Genetics and Molecular Biology Journals

Anna Melissa

genetics_molbio@omicsinc.com

1-702-714-7001 Extn: 9006

Immunology & Microbiology Journals

David Gorantl

immuno_microbio@omicsinc.com

1-702-714-7001Extn: 9014

Informatics Journals

Stephanie Skinner

omics@omicsinc.com

1-702-714-7001Extn: 9039

Material Sciences Journals

Rachle Green

materialsci@omicsinc.com

1-702-714-7001Extn: 9039

Mathematics and Physics Journals

Jim Willison

mathematics_physics@omicsinc.com

1-702-714-7001 Extn: 9042

Medical Journals

Nimmi Anna

medical@omicsinc.com

1-702-714-7001 Extn: 9038

Neuroscience & Psychology Journals

Nathan T

neuro_psychology@omicsinc.com

1-702-714-7001Extn: 9041

Pharmaceutical Sciences Journals

John Behannon

pharma@omicsinc.com

1-702-714-7001Extn: 9007

Social & Political Science Journals

Steve Harry

social_politicalsci@omicsinc.com

1-702-714-7001 Extn: 9042

 
© 2008-2016 OMICS International - Open Access Publisher. Best viewed in Mozilla Firefox | Google Chrome | Above IE 7.0 version