Date post: | 07-Apr-2016 |
Category: |
Documents |
Upload: | stm-journals-publication |
View: | 218 times |
Download: | 2 times |
Research & Reviews Journal of
Bioinformatics
STM JOURNALSScientific Technical Medical
(RRJoBI)
Jan - April 2014
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.
Focus and Scope Covers
is published (frequency: three times a year) in India by STM Journals
(division of Consortium e-Learning Network Private Ltd. Pvt.) 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 ([email protected])
Research & Reviews: A Journal of Bioinformatics
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
?Statistical analysis, staochastic grammars
STM Publication(s)
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 [email protected]
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:
[email protected]; Tel : +91 0120-4781211.
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
Himani 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 RajDistinguished Scientist & Director,
Indira Gandhi Centre for Atomic Research
(ICGAR)Kalpakkam, 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.
Prof. Sundara RamaprabhuProfessor, Department of Physics
Indian Institute of Technology Madras, India.
Dr. Shrikant Balkisan DhootHead Research & Development,
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
STM Journal 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
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 (1)] of Journal of
Bioinformatics. The intension of JoBI 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. JoBI 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. Computational Analysis of Microarray Gene Expression Profiling in Leishmania donovani and Leishmania major Ganesh Chandra Sahoo, Sindhuprava Rana, Manas Ranjan Dikhit, Md Yousuf Ansari, Pradeep Das 1
2. Computational Investigation of nsSNPs of PRSS1 Gene Ekta Kumari, Dhwani Raghaw, Jitendra Singh Rathore 15
3. Detection and Comparative Analysis of Uber-operons of FabZ gene Responsible for Fatty Acid Biosynthesis in Nostoc Punctiforme CyanobacteriumLakshmi P.T.V., Sathya Priya, Annamalai A. 23
4. Insilico Modelling and Comparative Docking Studies of EWS-FLI1 Responsible for Ewing Sarcoma in Human Beings Lakshmi PTV, Pragna Lakshmi T, Annamalai A 36
ContentsResearch & Reviews: A Journal of Bioinformatics
RRJoBI (2014)© STM Journals 2014. All Rights Reserved
Research & Reviews: A Journal of Bioinformatics
Volume 1, Issue 1
www.stmjournals.com
Computational Analysis of Microarray Gene Expression
Profiling in Leishmania donovani and Leishmania major
Ganesh Chandra Sahoo1, 2
*, Sindhuprava Rana1, Manas Ranjan Dikhit
1,
Md Yousuf Ansari1, 2
, Pradeep Das1, 2
1Biomedical Informatics Centre, RMRIMS, (ICMR), Agam Kuan, Patna, India
2Pharmacoinformatics Department, NIPER, Industrial Area, Hajipur, India
Abstract Leishmaniasis is one of the most deadly diseases in which the human genes are affected and gets altered expression. The genes of Leishmania species which are responsible for
causing leishmaniasis are not known yet. The objective behind this study is to know
about the genes which are differentially expressed (DE) when macrophage of mice is
infected with Leishmania donovani and Leishmania major. It also aims to know the
similarities of these DE genes from human genes and predict the genes responsible for leishmaniasis in human. Microarray data analyses allow us to monitor thousands of
genes simultaneously. The analyses of microarray data using statistical methods
predict the differentially expressed genes in diseased state. Clustering of these genes and functional analysis through GO database accentuate the predictions.
Keywords: Differentially Expressed (DE), Automated Robust Microarray Data
Analysis (ARMADA), Perfect Match (PM), Gene Ontology (GO), Clustering
RRJoBI (2014)© STM Journals 2014. All Rights Reserved
Research & Reviews: A Journal of Bioinformatics
Volume 1, Issue 1
www.stmjournals.com
Computational Investigation of nsSNPs of PRSS1 Gene
Ekta Kumari*, Dhwani Raghaw, Jitendra Singh Rathore
Department: School of Biotechnology, Gautam Buddha University, Greater Noida,
Gautam Buddha Nagar, U.P., India
Abstract This research is done for the prioritizing of SNPs of a gene PRSS1 causing hereditary
pancreatitis. In this analysis, the authors found out some nsSNPs as less stable,
deleterious, probably damaging retain high risk score. It was also predicted that SIFT is fast SNPs server with comparison of PolyPhen2. By Doing its energy calculation and
stability prediction, we can also determine the stability of mutant protein, that is ok whether this substitution is stable and heritable as it causes the hereditary pancreatitis.
We can also know about its RMSD value which helps in protein modeling in a way by
describing its structure features. Prioritizing nsSNPs in the investigation personalized medicine also as every SNPSs id having with their unique amino acid substitution at
unique position. Animal models or cell lines to determine if functionality of the protein has indeed been altered today with the help of nsSNPSs analysis and by calculating its
stability of protein are under selection pressure as it helps us in predicting phenotype
so it may be used in nsSNPs investigation and protein stability prediction in post-biology study.
Keywords: nsSNP, SIFT, mutant protein, protein stability
RRJoBI (2014)© STM Journals 2014. All Rights Reserved
Research & Reviews: A Journal of Bioinformatics
Volume 1, Issue 1
www.stmjournals.com
Detection and Comparative Analysis of Uber-operons of
FabZ gene Responsible for Fatty Acid Biosynthesis in
Nostoc Punctiforme Cyanobacterium
Lakshmi P.T.V.1*
, Sathya Priya1, Annamalai A.
2
1Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
2Department of Biotechnology, School of Biotechnology and Health Sciences, Karunya University,
Karunya Nagar, Coimbatore , Tamil Nadu, India
Abstract The increasing price of petroleum products has necessitated the development of
alternative fuel energy. The long alkyl chains that represent nature’s ‘petroleum’, are today isolated from microbes, plant and animal oils by amore scalable, controllable
and economic routes.Hence, in this perspective, the present study was aimed at
exploring the uber-operons of FabZ gene responsible for the synthesis of fatty acid in an aquatic nitrogen-fixing and filamentous cyanobacterium called Nostoc punctiforme.
Rearrangement of genomes occur randomly and frequently during evolution. Prokaryotic organisms maintain genes of similar function and that are involved in the
same cellular process in clusters of same transcriptional orientation and regulation.
The uber-operons are the set of functionally related genes maintained in close proximity in the genome, which assist in genome annotation and the discovery of
regulatory elements. Thus, the main objective of the study was to identify the genes
those were associated as uber-operon in the fatty acid pathway of Nostoc punctiforme and also to check for its involvement in different pathways based on the
‘neighbourhoods’ assembly and phylogeny.
Keywords: Biofuel, renewable resources, Fatty acids, Uber-operons,
Cyanobacterium
RRJoBI (2014) 36-45 © STM Journals 2014. All Rights Reserved Page 36
Research & Reviews: A Journal of Bioinformatics
Volume 1, Issue 1
www.stmjournals.com
Insilico Modelling and Comparative Docking Studies
of EWS-FLI1 Responsible for Ewing Sarcoma
in Human Beings
Lakshmi PTV1*, Pragna Lakshmi T
1, Annamalai A
2
1Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry
2Department of Biotechnology , School of Biotechnology and Health Sciences,
Karunya University , Karunya Nagar, Coimbatore , Tamilnadu , India
Abstract Ewing’s sarcoma (EWS) is a small round-cell tumor typically arising in the bones, rarely
in soft tissues, of children and adolescents. Patho-genomic translocations involving the EWS gene on chromosome 22 and an ETS-type gene (Fli1) on chromosome 11, are
implicated in more than 95% of Ewing’s sarcomas. A chimeric transcript that consists of
the N-terminus of EWS i.e., Transcriptional Activation Domain is fused to the C-terminal portion of FLI1 i.e., DNA Binding Domain (DBD). In this present study, the structure of
disordered fusion protein, EWS-FLI1 was predicted, modelled and refined. Ligand structures were drawn by using CHEMDRAW and CORINA. Comparative Docking
studies were performed for EWS-FLI1 protein with EMODIN and YK-4-279 by using
SCHRODINGER. Although, EMODIN and YK-4-279 interacted with the protein by establishing the H-Bonds with SER 316, GLN 326, GLN 328, ASP 430 by the former and
with SER 316, ALA 110, and GLN 109 with the later, a common residue of SER 316 was
observed to be interacting. However, the docking score and Glide g score of -6.278203 and -6.100573 were observed for EMODIN and YK-4-279 respectively, which revealed
EMODIN to be much more effective in presenting the highest value. Molecular Dynamics Simulation was performed to analyse the stability of Docked structure of
protein and ligand. For EMODIN, the stabilized structure was formed at 646 ps whereas
for YK-4-279, the stabilized structure was formed at 680 ps and RMSD values for EMODIN was comparatively lower than YK-4-279.
Keywords: Ewing sarcoma, disordered fusion protein, natural ligand, comparison,
molecular dynamic simulation