eISSN: 2393 - 8722 May - August 2014
Research & Reviews: A Journal of
Bioinformatics (RRJoBI)
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Editorial Board Dr. Afroz Alam Assistant 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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Dr. Pankaj Chetia Research Associate , Bioinformatics Centre Department of Life Science & Bioinformatics Assam University, Silchar, Assam, India.
Dr. Pranav Shah Associate Professor, Maliba Pharmacy College, Maliba Campus, Surat, Gujarat, India.
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STM JOURNALS
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
Research & Reviews: A Journal of Bioinformatics
Contents
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 Level Rajpal 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
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)Š 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 B-galactosidase
genes,
FASTA,
NCBI/Gen
Bank
Database,
RRJoBI (2014) Š STM Journals 2014. All Rights Reserved
Clustal W,
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)Š 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
RRJoBI (2014)Š STM Journals 2014. All Rights Reserved