Research & reviews journal of computational biology (vol3, issue3) by STM Journals Publication

ISSN: 2349-3720 ISO: 9001Certified

STM Journals Empowering knowledge

Research & Reviews: Journal of Free Online Registration

Computational Biology (RRJoCB)

September - December 2014 /

Energy /

/ Instrumentation /Science

GLOBAL READERSHIP STATISTICS

conducted

Over 500 Indian and International Subscribers. 30,000 Top Researchers, Scientists, Authors and Editors All Over the World Associated. Editorial/ Reviewer Board Members : 1000+. 1,00,000+ Visitors to STM Website From 140+ Countries Quarterly. 10,000 + Downloads from STM Website.

STM Journals invites the papers from the National Conferences, International Conferences, Seminars conducted by Colleges, Universities, Research Organizations etc. for Conference Proceedings and Special Issue. 타Special Issues come in Online and Print versions. 타STM Journals offers schemes to publish such issues on payment and gratis (online) basis as well.

To g e t m o r e i n f o r m a t i o n : stmconferences.com

STM JOURNALS Scientific

Technical

Medical

www.stmjournals.com

STM Publication(s) 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. Objectives of STM Publication(s): ? Scientific, Technical and Medical research promotions. ? Publication of genuine Research/Review, Short Articles and Case Studies through proper review

process. ? Publishing Special Issues on Conferences. ? Preparing online platform for other print Journals. ? Empowering the libraries with online and print Journals in Scientific, Technical and Medical

domains. ? Publishing and distribution of books on various subjects which mainly falls in the category of

Nanotechnology, Scientific and technical writing & Environment, Health and Safety. Salient Features: ? A bouquet of 100+ Journals that fall under Science, Technical & Medical domains. ? Employs Open Journals System (OJS) A Journal Management & Publishing System. ? The first and one of the fastest growing publication website in India as well as in abroad for its quality

and coverage. ? Rapid online submission and publication of papers, soon after their formal acceptance/ finalization. ? Facilitates linking with the other authors or professionals. ? Worldwide circulation and visibility.

Research & Reviews : Journal of Computational Biology (ISSN: 2349-3720) Focus and Scope Covers ? Organization and Drug designing tools for development analysis ? Parallel Computation, Linking Disparate Databases, Data Mining ? Biological software design and development ? Molecular Modeling ? Biological Algorithms Development and Implementation ? Biological Databases Development ? Bioinformatics, Statistical application in Genetics and Molecular biology

Research & Reviews : Journal of Computational Biology is published (frequency: three times a year) in India by STM Journals (division of Consortium e-Learning Network Private Ltd.) The views expressed in the articles do not necessarily reflect of the Publisher. The publisher does not endorse the quality or value of the advertised/sponsored products described therein. Please consult full prescribing information before issuing a prescription for any products mentioned in this publication. No part of this publication may be reproduced, stored in retrieval system or transmitted in any from without written permission of the publisher. To cite any of the material contained in this Journal, in English or translation, please use the full English reference at the beginning of each article. To reuse any of the material, please contact STM Journals (info@stmjournals.com)

STM Journals (division of Consortium e-Learning Network Private Ltd. ) having its Marketing office located at Office No. 4, First Floor, CSC pocket E Market, Mayur Vihar Phase II, New Delhi-110091, India is the Publisher of Journal. Statements and opinions expressed in the Journal reflect the views of the author(s) and are not the opinion of STM Journals unless so stated. Subscription Information and Order: Cost of Journal: ? National Subscription: Rs. 3750/- per Journal (includes 3 print issues), Single Issue copy purchase Rs.1500/copy ? International Subscription: ? Online Only- $99, Print Only-$149 (includes 3 print issues) ? Online + Print-$199 (includes 3 print issues + online access of published back volumes )

To purchase print compilation of back issues please send your query at info@stmjournals.com Subscription must be prepaid. Rates outside the India includes speed delivery charges. Prices subject to change without notice. Mode of Payment: At par cheque, Demand draft, and RTGS (payment to be made in favor of Consortium E-Learning Network. Pvt. ltd., payable at Delhi/New Delhi. Online Access Policy A). For Authors: In order to provide maximum citation and wide publicity to the authors work, STM Journals also have Open Access Policy, authors who would like to get their work open access can opt for Optional Open Access publication at nominal cost as follows India, SARC and African Countries: INR 2500 or 100 USD including single hard copy of Author's Journal. Other Countries: USD 200 including single hard copy of Author's Journal. B). For Subscribers: ? Online access will be activated within 72 hours of receipt of the payment (working days), subject to receipt of

correct information on user details/Static IP address of the subscriber. ? The access will be blocked: ? If the user requests for the same and furnishes valid reasons for blocking. ? Due to technical issue. ? Misuse of the access rights as per the access policy.

Advertising and Commercial Reprint Inquiries: STM Journals with wide circulation and visibility offer an excellent media for showcasing/promotion of your products/services and the events-namely, Conferences, Symposia/Seminars etc. These journals have very high potential to deliver the message across the targeted audience regularly with each published issue. The advertisements on bulk subscriptions, gift subscriptions or reprint purchases for distribution etc. are also very welcome. Lost Issue Claims: Please note the following when applying for lost or missing issues: ? Claims for print copies lost will be honored only after 45 days of the dispatch date and before publication of the

next issue as per the frequency. ? Tracking id for the speed post will be provided to all our subscribers and the claims for the missing Journals will

be entertained only with the proofs which will be verified at both the ends. ? Claims filed due to insufficient (or no notice) of change of address will not be honored. ? Change of Address of Dispatch should be intimated to STM Journals at least 2 months prior to the dispatch

schedule as per the frequency by mentioning subscriber id and the subscription id. ? Refund requests will not be entertained.

Legal Disputes All the legal disputes are subjected to Delhi Jurisdiction only. If you have any questions, please contact the Publication Management Team: info@stmjournals.com; Tel : +91 0120-4781211.

Publication Management Team Chairman Mr. Puneet Mehrotra Managing Director STM Journals, Consortium eLearning Network Pvt. Ltd.(CELNET) Noida ,India

Group Managing Editor Dr. Archana Mehrotra Director CELNET, Delhi, India

Internal Members Puneet Pandeya Manager

Monika Malhotra Assistant Manager

Associate Editors Gargi Asha Jha Nupur Anand Shikha Suman

Assistant Editors Priyanka Aswal Aditya Sanyal Deepika Bhadauria Sona Chahal Himani Pandey

External Members

Dr. Bimlesh Lochab Industrial Tribology Machine Dynamics & Maintenance Engineering Centre (ITMMEC) Indian Institute of Technology Delhi, India.

Dr. Rajiv Prakash School of Materials Science and Technology, Institute of Technology, Banaras Hindu University, Varanasi, India.

Prof. S. Ramaprabhu Alternative Energy Technology Laboratory, Department of Physics, Indian Institute of Technology, Chennai, India.

Dr. Rakesh Kumar Assistant Professor, Department of Applied Chemistry, BIT Mesra, Patna, India.

STM Journal (s) Advisory Board

Dr. Ashish Runthala

Prof. Bankim Chandra Ray

Lecturer, Biological Sciences Group, Birla Institute of Technology & Science, Pilani Rajasthan, India.

Professor and Head, Department of Metallurgical and Materials Engineering National Institute of Technology, Rourkela, India.

Dr. Baldev Raj

Prof. D. N. Rao

Distinguished Scientist & Director, Indira Gandhi Centre for Atomic Research (ICGAR)Kalpakkam, India.

Dr. Baskar Kaliyamoorthy Associate Professor, Department of Civil Engineering National Institute of Technology Trichy, India.

Dr. Hardev Singh Virk Professor Emeritus, Eternal University, Baru Sahib, India.

Professor, Department of Biochemistry, AIIMS, New Delhi, India.

Prof. Jugal Kishore Professor, Department of Community Medicine, Maulana Azad Medical College, New Delhi, India.

Dr. Pankaj Poddar Scientist, Physical & Materials Chemistry Division, National Chemical Laboratory, Pune, India.

Dr. Nandini Chatterjee Singh Associate Professor, National Brain Research Centre, Manesar, India.

STM Journal (s) Advisory Board

Dr. Priyavrat Thareja

Dr. Rakesh Kumar

Head, Materials and Metallurgical Engineering department, PEC University of Technology, Chandigarh, India.

Assistant Professor, Department of Applied Chemistry, BIT Mesra, Patna, India

Dr. Shankargouda Patil

Dr. Shrikant Balkisan Dhoot

Asst. Prof., Department of Oral Pathology, KLE Society's Institute of Dental Sciences, Bangalore, India.

Head Research & Development, Nurture Earth R&D Pvt Ltd MIT Campus, Beed bypass road, Aurangabad, India.

Prof. Subash Chandra Mishra

Prof. Sundara Ramaprabhu

Professor, Metallurgical & Materials Engineering Department, NIT, Rourkela, India.

Professor, Department of Physics Indian Institute of Technology Madras, India.

Prof. Yuwaraj Marotrao Ghugal Professor and Head Department, Govt. College of Engineering Station Road, Osmanpura, Aurangabad, India.

Editorial Board

Dr. Jagadeesha Maharudraiah Institute of Bioinformatics, Bangalore, India.

Joseph Selvin Drug Discovery and Development Research Unit (DDRU), Dept. of Bioinformatics, India.

Dr. Khushhali Menaria Department of Bioinformatics, Maulana Azad National Institute of Technology, Bhopal (M.P.), India.

Dr. Ayaluru Murali Bioinformatics Centre, Pondicherry University, India.

P. Chellapandi Department of Bioinformatics, Centre for Excellence in School of Life Sciences, Bharathidasan University, Tiruchirappalli, India.

Dr. Amutha Ramaswamy Centre for Bioinformatics, Pondicherry University Campus, Pondicherry, India.

Prof.(Dr.) Jugal Kishore Department of Community Medicine, Maulana Azad Medical College, New Delhi 110002, India.

Dr. Kumud Sarin Educational Consultant, New Delhi, India

Director's Desk

STM JOURNALS

I take the privilege to present the hard copy compilation for the Volume 3 Issue (3) of Research & Reviews: Journal of Computational Biology (RRJoCB). The intension of RRJoCB is to create an atmosphere that stimulates creativeness, research and growth in the area of Computational Biology. The development and growth of the mankind is the consequence of brilliant Research done by eminent Scientists and Engineers in every field. RRJoCB provides an outlet for Research findings and reviews in areas of Computational Biology 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 Computational Biology. Finally, I express my sincere gratitude and thanks to our Editorial/ Reviewer board and Authors for their continued support and invaluable contributions and suggestions in the form of authoring writeups/ 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/Reviesw 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 : Journal of Computational Biology

Contents

1. Phylogenetic Analysis of Antigenic Variability in Klebsiella pneumoniae against Antibacterial Ocular Drugs S. Umadevi, P. M. Ayyasamy, S. Rajakumar

2. Algorithm for Early Detection of Genetic Fusion in Cancer, Tumors and Chronic Bacterial Infection Ankush Rai

3. Statistical Implementation of the Plant Functional Traits of Bacopa monnieri and Their Biological Interpretation Shikha Suman

Research & Reviews: Journal of Computational Biology ISSN: 2319-3433 (online), ISSN: 2349-3720 (print) Volume 3, Issue 3 www.stmjournals.com

Phylogenetic Analysis of Antigenic Variability in Klebsiella pneumoniae against Antibacterial Ocular Drugs S. Umadevi 1, P. M. Ayyasamy2, S. Rajakumar1* 1

Department of Marine Biotechnology, Bharathidasan University, Tiruchirappalli, India 2 Department of Microbiology, Periyar University, Salem, India

Abstract Klebsiella pneumonia, associated with significant proportion of hospital-acquired urinary tract infections, pneumonia, soft tissue infections, liver abscess, endophthalmitis and meningitis. Though the antibiotic eye drops against K. pneumoniae are available, immunologically distinct strains evolved by mutations in epitopes and leads resistance to ocular antibacterial drugs. The analysis of escape mutation necessitates new drug development.Also, it constitutes a major challenge to effective drug design. In present work, molecular basis of antigenic resistance in K. pneumoniae against the antibacterial ocular drugs was investigated. The resistance genes were identified and identified that genetic drift was found in 16 genes and higher number of mutaionswas found in class-A beta-lactamase.The protein sequences of class-A beta-lactamase from resistance strains were obtained and antigenic variability was carried out in terms of antigenic distance based on the sequence alignment and phylogenetic analysis. Moreover the docking study of protein with drug molecules was done in order to find out whether the mutations are at active site or at other residues.It was found that, mutations were dispersed throughout the sequence, and were not found at a particular segment. The escape mutation was found less at active site than rest. It concludes that the mutations in non-active residues may leads to changes in electrostatic and steric interactions. In this work, drift was analyzed in class-A beta-lactamase alone, the overall analysis may play potential role in effective designing of antibacterial drug against K. pneumoniae.

Keywords: Antigenic variability, Class-A beta-lactamase, Klebsiella pneumonia, ocular drugs, phylogeny

Research & Reviews: Journal of Computational Biology ISSN: 2319-3433 (online), ISSN: 2349-3720 (print) Volume 3, Issue 3 www.stmjournals.com

Algorithm for Early Detection of Genetic Fusion in Cancer, Tumors and Chronic Bacterial Infection Ankush Rai* Department of Applied Science, CRIAD Laboratories, Smiriti Nagar, Bhilai 490020, Chhattisgarh, India Abstract In the present study we have designed an algorithm for early detection of DNA fusion to discover the potential transcription which embodies the fusion of gene products derivable from the human DNA with that of bacterial and cancerous viruses, resulting from the several breakage points and reassembling of different chromosomes, or that of within a chromosome. Without relying on existing annotations the proposed algorithm proves its efficacy in detecting alignment of RNA sequences from unannotated splice variants of known genome strands. Using this algorithm in the age of Big Data analytics the potential threat of cancer, tuberculosis, tumors, and asthma can be predicted beforehand while scaling such effects, ranging from individual to population scale. We have also reported the results of the algorithm for over 900 samples with solid supporting evidences and opens a new virotherapy approach of numerically quantized cure for disease like cancer, tumors and asthma.

Keywords: Algorithm, computational modeling, gene fusion, DNA transcription

Research & Reviews: Journal of Computational Biology ISSN: 2319-3433 (online), ISSN: 2349-3720 (print) Volume 3, Issue 3 www.stmjournals.com

Statistical Implementation of the Plant Functional Traits of Bacopa monnieri and Their Biological Interpretation Shikha Suman* Department of Botany, Banaras Hindu University, Varanasi, India Abstract The plat functional traits are interdependent and correlated, a single molecule or a smaller plant character may alter the whole physiology. This work is based on the statistical prove of the interdependence of the plant character in governing the life cycle and their biological interpretation. In this article, all the characters are statically correlated and depicted the main factors governing the prime function of the plant.

Keywords: Relative growth rate, correlation, biostatistical, plant functional traits