Research & Reviews: A Journal of

Bioinformatics

STM JOURNALSScientific Technical Medical

(RRJoBI)

May - August 2014

eISSN: 2393 - 8722

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Research & Reviews: A Journal of Bioinformatics

eISSN: 2393-8722

Research & Reviews: A Journal of Bioinformatics

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Industrial Tribology Machine Dynamics & Maintenance

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Indian Institute of Technology Delhi, India

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Alternative Energy Technology Laboratory,

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Dr. Monika DalalSenior Scientist at National Research

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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.

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Laboratory Center for Bioinformatics School of Life Sciences

Pondicherry University, India.

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Sciences, SHIATS-Demeed University, Allahabad, India.

Dr. Pankaj ChetiaResearch Associate , Bioinformatics

Centre Department of Life Science & Bioinformatics Assam University,

Silchar, Assam, India.

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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