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Research & Reviews: A Journal of
Bioinformatics
STM JOURNALSScientific Technical Medical
(RRJoBI)
May - August 2014
eISSN: 2393 - 8722
STM Publication, a strong initiative by Consortium E-Learning Network Private ltd.(Estd. 2006) was launched in the
year 2010 under the support and guidance by our esteemed Editorial and Advisory board members from renowned
institutes.
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Research & Reviews: A Journal of Bioinformatics
eISSN: 2393-8722
Research & Reviews: A Journal of Bioinformatics
?Sequence database and Sequence Alignment
?Sequence mining , Sequence profiling
?System biology
?Biological networks , protein –protein interaction networks
? DNA Assembly, Clustering , Mapping
?Phylogeny reconstruction algorithms
? Protein Structure predictions
?Silico technology
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Chairman
Mr. Puneet Mehrotra
Managing Director STM Journals, Consortium eLearning Network Pvt. Ltd.(CELNET)
Noida ,India
Group Managing Editor Dr. Archana Mehrotra
DirectorCELNET, Delhi, India
Puneet Pandeya
ManagerMonika Malhotra
Assistant Manager
Assistant Editors
Aditya Sanyal
Anupama Garg
Himani Pandey
Publication Management Team
Internal Members
External Members
Dr. Bimlesh Lochab
Industrial Tribology Machine Dynamics & Maintenance
Engineering Centre (ITMMEC)
Indian Institute of Technology Delhi, India
Prof. S. Ramaprabhu
Alternative Energy Technology Laboratory,
Department of Physics,
Indian Institute of Technology, Chennai, India
Dr. Rajiv Prakash
School of Materials Science and Technology,
Institute of Technology, Banaras Hindu University,
Varanasi, India
Dr. Rakesh Kumar
Assistant Professor, Department of
Applied Chemistry, BIT Mesra,
Patna, India
Associate Editors
Gargi Asha Jha
Nupur Anand
Priyanka Aswal
Sona Chahal
STM Journal (s) Advisory Board
Dr. Ashish RunthalaLecturer, Biological Sciences Group,
Birla Institute of Technology & Science, Pilani Rajasthan, India.
Dr. Baldev Raj
Former Director, Indira Gandhi Centre for Atomic Research, India.
Chairman, National Institute of Technology Puducherry, India.
Dr. Baskar KaliyamoorthyAssociate Professor, Department
of Civil Engineering National Institute of Technology Trichy, India.
Prof. Bankim Chandra RayProfessor and Head, Department of
Metallurgical and Materials Engineering National Institute of Technology,
Rourkela, India.
Prof. D. N. Rao Professor, Department of Biochemistry,
AIIMS, New Delhi, India.
Prof. Jugal KishoreProfessor, Department of Community
Medicine, Maulana Azad Medical College, New Delhi, India.
Dr. Pankaj PoddarScientist, Physical & Materials ChemistryDivision, National Chemical Laboratory,
Pune, India.
Dr. Hardev Singh VirkProfessor Emeritus, Eternal
University, Baru Sahib, India.
Dr. Nandini Chatterjee SinghAssociate Professor,
National Brain Research Centre, Manesar, India.
Dr. Shankargouda PatilAsst. Prof., Department of Oral
Pathology, KLE Society's Institute of Dental Sciences, Bangalore, India.
Prof. Subash Chandra MishraProfessor, Metallurgical & Materials
Engineering Department, NIT, Rourkela, India.
Prof. Yuwaraj Marotrao GhugalProfessor and Head Department, Govt.College of Engineering Station Road,
Osmanpura, Aurangabad, India.
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Indian Institute of Technology Madras, India.
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Nurture Earth R&D Pvt LtdMIT Campus, Beed bypass road,
Aurangabad, India.
Dr. Rakesh KumarAssistant Professor,
Department of Applied Chemistry, BIT Mesra, Patna, India.
Dr. Priyavrat TharejaHead, Materials and Metallurgical
Engineering Department, PEC University of Technology,
Chandigarh, India.
STM Journal (s) Advisory Board & Editorial Board
Dr. Uday MuddapurProfessor, Department of Biotechnology Engineering, Dr. M.S Sheshgiri college
of Engineering and Technology, Belgaum, India.
Viral Dineshchandra JagiwalaAssistant Professor,
Shree Dhanvantary Pharmacy College, Surat, Gujarat, India
Dr Ashwin Laxmikant KotnisAssistant Professor, Department of
Biochemistry, AIIMS, Saket Nagar, Bhopal, India.
Dr. Monika DalalSenior Scientist at National Research
Centre on Plant Biotechnology, New Delhi, India.
Editorial Board
Dr. Afroz AlamAssistant Professor (S.G.) Department of
Bioinformatics, Karunya University, Coimbatore,
Tamil Nadu, India.
Dr. Bharat Bhusan Subudhi Associate Professor, School of
Pharmaceutical Sciences, Siksha O Anusandhan University,
Bhubaneswar, India.
Dr. Lakshmi AnnamalaiAssociate Professor, Phytomatics
Laboratory Center for Bioinformatics School of Life Sciences
Pondicherry University, India.
Dr. Nooruddin KhanAssistant Professor, Department of Biotechnology and Bioinformatics,
University of Hyderabad, Hyderabad, Andhra Pradesh, India.
Dr. Jitendra Singh RathoreAssistant Professor of Microbiology on
Visiting Track, Department of Microbiology Perelman,
University of Pennsylvania, Philadelphia.
Dr. Amita VermaHead Deptarment of Pharmaceutical
Sciences, SHIATS-Demeed University, Allahabad, India.
Dr. Pankaj ChetiaResearch Associate , Bioinformatics
Centre Department of Life Science & Bioinformatics Assam University,
Silchar, Assam, India.
Dr. Paramananda SaikiaAssistant Professor, University of
Hyderabad, Hyderabad, India.
Dr. Pranav ShahAssociate Professor, Maliba Pharmacy
College, Maliba Campus, Surat, Gujarat, India.
Dr. Roshan MakamAssociate Professor & Head ,Biotechnology Department, PES Institute of Technology,
Bangalore, India.
Dr. S. K. M. HabeebAssistant Professor, Department of
Bioinformatics, School of Bioengineering, Kattankulathur Campus,
SRM University, India
Dr. Sandeep Gupta
Research Scientist (NDSSL) Virginia Polytechnic Institute and State
University, Pratt Drive.
I take the privilege to present the print version for the [Volume 1 Issue (2)] of Research & Reviews: A
Journal of Bioinformatics. The intension of RRJoBI is to create an atmosphere that stimulates
creativeness, research and growth in the area of Bioinformatics.
The development and growth of the mankind is the consequence of brilliant Research done by
eminent Scientists and Engineers in every field. RRJoBI provides an outlet for Research findings and
reviews in areas of Bioinformatics found to be relevant for National and International recent
developments & research initiative.
The aim and scope of the Journal is to provide an academic medium and an important reference for
the advancement and dissemination of Research results that support high level learning, teaching and
research in the domain of Bioinformatics.
Finally, and Authors for their continued support and invaluable contributions and suggestions in the
form of authoring I express my sincere gratitude and thanks to our Editorial/ Reviewer board write
ups/ reviewing and providing constructive comments for the advancement of the journals. With
regards to their due continuous support and co-operation, we have been able to publish quality
Research/Reviews findings for our customers base.
I hope you will enjoy reading this issue and we welcome your feedback on any aspect of the Journal.
Dr. Archana Mehrotra
Director
STM Journals
Director's Desk
STM JOURNALS
1. Pharmacophore Mapping of Dengue Virus Inhibitors of Natural Origin Using Phase and Self Organizing Neural Networks Chinnu Sunny, Md. Afroz Alam 1
2. Comparative Genomics of Heat Shock Protein in Pathogenic Bacteria Jenifer S. 19
3. Novel Activity of NrnA Homolog Signifies Engineering at Cellular LevelRajpal Srivastav 35
4. Structural Studies of Alternatively Sliced Transcript Isoforms in Context of Esophageal Cancer Vidyavati N. Deshpande, S.C. Mali, Uday M. Muddapur, V. G. Shanmuga Priya, Preeti Honagudi, Anita Vibhuti 38
ContentsResearch & Reviews: A Journal of Bioinformatics
RRJoBI (2014)© STM Journals 2014. All Rights Reserved
Research & Reviews: A Journal of Bioinformatics ISSN: 2393-8722 (online)
Volume 1, Issue 2
www.stmjournals.com
Pharmacophore Mapping of Dengue Virus Inhibitors of
Natural Origin Using Phase and Self Organizing
Neural Networks
Chinnu Sunny, Md. Afroz Alam* Department of Bioinformatics, Karunya University, Karunya Nagar, Coimbatore, Tamil Nadu, India
Abstract Dengue virus (DENV) infection is an important arthropod-born viral infection infecting
about 2.5 billion people worldwide. To date there are no effective vaccine or antiviral treatment for dengue. Dengue patients are usually supportively treated until they recover
without any specific treatment measures. Plants and plant’s derived compounds remain an important source for the discovery and the development of new antiviral drugs
because of their expected low side effects and their high accessibility in the nature. Thirty
one compounds have been identified from literatures which are known to inhibit the virus. But the action or orientation of these compounds on the receptor are unknown. So
docking studies and pharmacophore model generation were carried out using these
compounds and a known receptor NS2B-NS3 pro of dengue virus. Most of the compound exhibited good docking results among which Rutin showed the best docking score and
energy. Some other compounds which exhibited good properties were methyl gallate, 4 Hydroxypandruitin A and Hespertin. Pharmacophores were also generated which
exhibited the features of the receptor, with which these compounds interact.
Keywords: dengue virus, docking, pharmacophore, SOM
RRJoBI (2014) © STM Journals 2014. All Rights Reserved
Research & Reviews: A Journal of Bioinformatics ISSN: 2393-8722 (online)
Volume 1, Issue 2
www.stmjournals.com
Comparative Genomics of Heat Shock Protein
in Pathogenic Bacteria
Jenifer S.* Department of Biotechnology, Bon Secours College for Women, Thanjavur, TamilNadu, India
Abstract Genome comparison has recently become a common research topic in computer science.
The development of computer-assisted mathematics (using products such as Mathematica or Matlab) has helped engineers, mathematicians, and computer scientists to start
operating in this domain, and a public collection of case studies and demonstrations is
growing, ranging from whole genome comparisons to gene expression analysis. This has increased the introduction of different ideas, including concepts from systems and
control, information theory, strings analysis, and data mining. It is anticipated that computational approaches will become and remain a standard topic for research and
teaching, while students fluent in both topics start being formed in the multiple courses
created in the past few years. In the present investigation, four pathogenic microorganisms have been selected. They are (1) Salmonella typhimurium, (2) Bacillus
subtilis, (3) Mycobacterium tuberculosis, and (4) Thermoplasma acidophilum. In the above organisms, heat shock protein genes (HSP genes) sequences have been retrieved
from the Bioinformatics databases.
Keywords: HSP genes, FASTA, NCBI/Gen Bank Database, Clustal W, B-galactosidase
RRJoBI (2014)© STM Journals 2014. All Rights Reserved
Research & Reviews: A Journal of Bioinformatics ISSN: 2393-8722 (online)
Volume 1, Issue 2
www.stmjournals.com
Novel Activity of NrnA Homolog Signifies
Engineering at Cellular Level
Rajpal Srivastav*
Translational Health Science & Technology Institute, Gurgaon, Haryana, India
Abstract Exonuclease homolog protein cloned, expressed, purified and found to have multiple
exonuclease activities. This study highlights the importance of cellular engineering at
protein level, where one protein can do multiple functions under different conditions.
Keywords: exonuclease, homolog, NrnA, DNA replication, RecJ
RRJoBI (2014)© STM Journals 2014. All Rights Reserved
Research & Reviews: A Journal of Bioinformatics ISSN: 2393-8722 (online)
Volume 1, Issue 2
www.stmjournals.com
Structural Studies of Alternatively Sliced Transcript
Isoforms in Context of Esophageal Cancer
Vidyavati N. Deshpande*, S.C. Mali, Uday M. Muddapur, V. G. Shanmuga Priya,
Preeti Honagudi, Anita Vibhuti Department of Biotechnology, K.L.E. Dr. M. S. Sheshgiri College of Engineering and Technology,
Belgaum, Karnataka, India
Abstract Microarray one of the high throughput technologies is used to measure the gene expression, which serves as the primary source for different types of analysis. The results
of these experiments are stored in several repositories/databases of which many are made
publically available. GEO-Gene Expression Omnibus is one among them. Alternative
splicing is a regulated process whose deregulation influences cancer. In the present work,
the expression array data sets of esophageal tissue in Normal and Cancer conditions are
retrieved from GEO database and normalized to get the relevant data which is suitable for further analysis. Significant Branch point sequences were found out and also
significant splice site motifs are also recognized using an algorithm and excel operations.
Keywords: Esophageal cancer, Alternative splicing, splice Factors, Meta-Analysis,
GEO Database, Branch-point