International Journal of Computational Biology and Bioinformatics vol 2 issue 2 by JournalsPub

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20 mit icle b rt u S A Applied Mechanics r International Journal of Electro Mechanics and u Mechanical Behaviour International Journal of Machine Design and Yo Manufacturing

Mechanical Engineering

¬ International Journal of Thermal Energy and

¬ International Journal of Production Engineering ¬ International Journal of Industrial Engineering

« « «

Applications

International Journal of Mechanical Dynamics and Analysis International Journal of Fracture and damage Mechanics International Journal of Structural Mechanics and Finite Elements

and Design ¬ International Journal of Manufacturing and

Materials Processing ¬ International Journal of Mechanical Handling and

Automation 5 more...

Electronics and Telecommunication « International Journal of Radio Frequency Design « International Journal of VLSI Design and Technology « International Journal of Embedded Systems and Emerging

Technologies « International Journal of Digital Electronics « International Journal of Digital Communication and Analog

Chemical Engineering « International Journal of Renewable Energy and its

Commercialization « International Journal of Environmental Chemistry « International Journal of Agrochemistry « International Journal of Prevention and Control of Industrial

Pollution

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Architecture « International Journal of Housing and Human Settlement

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International Journal of Analog Integrated Circuits International Journal of Automatic Control System International Journal of Electrical Machines & Drives International Journal of Electrical Communication Engineering « International Journal of Integrated Electronics Systems and 4 more... Circuits « « « «

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International Journal of Computational Biology & Bioinformatics IJCBB

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International Journal of Immunological Nursing International Journal of Cardiovascular Nursing International Journal of Neurological Nursing International Journal of Orthopedic Nursing International Journal of Oncological Nursing

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International Journal of Energetic Materials International Journal of Bionics and Bio-Materials International Journal of Ceramics and Ceramic Technology International Journal of Bio-Materials and Biomedical Engineering 4 more...

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International Journal of Photochemistry International Journal of Analytical and Applied Chemistry International Journal of Green Chemistry International Journal of Chemical and Molecular Engineering 3 more...

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Biomaterials International Journal of Plant Biotechnology International Journal of Molecular Biotechnology International Journal of Biochemistry and Biomolecules International Journal of Animal Biotechnology and 3 more... Applications

Nanotechnology « International Journal of Applied Nanotechnology « International Journal of Nanomaterials and Nanostructures « International Journals of Nanobiotechnology

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International Journal of Computational Biology and Bioinformatics International Journal of Computational Biology and Bioinformatics is a concerning recent advancement and emerging technology in computational biology and bioinformatics. Journal also covers a wide range of topics including synthetic biology and structural genomics. Journal publishes both experimental and theoretical papers.

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Commissioning Editors Ankita Singh

Dr. Chhavi Goel

Deepika Bhadauria

Manisha Dhoble Rekha Rani

EDITORIAL BOARD MEMBERS Dr. P Mary Anupama Department of Biotechnology, ANITS, Sangivalasa, Visakhapatnam (A.P.), India

Dr. Ir. Sreenivas Reddy Bathula Department of Biotechnology, Bapuji Institute of Engineering & Technology, Karnataka, India

Dr. Xiaojun Chen Institute of Biomedical Manufacturing and Life Quality Engineering, Shanghai Jiao Tong University (SJTU), China

Dr. Nayira College of Medicine, Imam University, Saudi Arabia

Dr Rahul Raghavan Department of Biotechnology, University of Calicut, Kerala, India

Dr. Abid Qureshi Institute of Microbial Technology, Bioinformatics Center, Chandigarh, India

Dr. Divya Verma Department of Botany Kalindi College, University of Delhi New Delhi, India.

Dr. Aumreetam Dinabandhu ICAR - NRC on Plant Biotechnology, Pusa Campus, New Delhi, India

Dr. Sanjay Mahendrakumar Dave Department of Biotechnology, Hemchandracharya North Gujarat University, Gujarat, India

Ashish Runthala Department of Biological Sciences, Birla Institute of Technology & Science Rajasthan, India

From the Editor's Desk Dear Readers, We would like to present, with great pleasure, the inaugural volume of a new scholarly journal, International Journal of Computational Biology and Bioinformatics. This journal is part of the Applied Sciences, and is devoted to the scope of present Computational Biology and Bioinformatics issues, from theoretical aspects to application-dependent studies and the validation of emerging technologies. This new journal was planned and established to represent the growing needs of Computational Biology and Bioinformatics as an emerging and increasingly vital field, now widely recognized as an integral part of scientific and technical investigations. Its mission is to become a voice of Computational Biology and Bioinformatics, addressing researchers and practitioners in this area. The core vision of International Journal of Computational Biology and Bioinformatics in JournalsPub is to propagate novel awareness and know-how for the profit of mankind ranging from the academic and professional research societies to industry practitioners in a range of topics in Computational Biology and Bioinformatics in general. JournalsPub acts as a pathfinder for the scientific community to publish their papers at excellently, well-timed & successfully. International Journal of Computational Biology and Bioinformatics focuses on original high-quality research in the realm of Computer simulation, Mathematical biology, Molecular modeling, Network biology, Structural genomics, Synthetic biology, Systems biology, Bioinformatics, Computational genomics and proteomics, Biomedical image processing, Modelling and simulation, Sequence assembly, search, and alignment, Computational biomedical data engineering etc. The Journal is intended as a forum for practitioners and researchers to share the techniques of Computational Biology and Bioinformatics and solutions in the area. Many scientists and researchers have contributed to the creation and the success of Computational Biology and Bioinformatics. We are very thankful to everybody within that community who supported the idea of creating an innovative platform. We are certain that this issue will be followed by many others, reporting new developments in the field of Computational Biology and Bioinformatics. This issue would not have been possible without the great support of the Editorial Board members, and we would like to express our sincere thanks to all of them. We would also like to express our gratitude to the editorial staff of JournalsPub, who supported us at every stage of the project. It is our hope that this fine collection of articles will be a valuable resource for Computational Biology and Bioinformatics readers and will stimulate further research into the vibrant area of Computational Biology and Bioinformatics. Puneet Mehrotra Managing Director

Contents 1. Postural State Assessment during Quiet and Sensory â&#x20AC;&#x201C; Conflicted Stance through EEG Neha Hooda, Neelesh Kumar

2. In Silico Single Nucleotide Polymorphism Analysis in Human Glutamate Dehydrogenase Usra Latief, Vivek Dhar Dwivedi

3. Effect of Gender and Performance on EMG Activity of Selected Knee Extensor Muscles during Isometric Contractions of Fully Extended Knee in Athletes Manvinder Kaur, Sanjeev Nara, Sateesh Reddy Avutu, Dinesh Bhatia, Dhananjoy Shaw

4. Analysis of Ground Reaction Force and Temporal Parameters during Human Gait for Design of Sensor Mechanism Ratan Das, Devendra Mohan, Pallabi Baruah, Neelesh Kumar

5. A Review on Principles of Bioinformatics and Its Methods Based on Sequence Techniques Sona Singh

International Journal of Computational Biology and Bioinformatics

Vol. 2: Issue 2

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Postural State Assessment during Quiet and Sensory â&#x20AC;&#x201C; Conflicted Stance through EEG Neha Hooda*, Neelesh Kumar

Biomedical Instrumentation Division, CSIR-CSIO, Chandigarh, India

ABSTRACT The body balance is not totally sub-cortically controlled. It results from a qualitative and congruent sensory input from three major sources, namely visual, proprioceptive and vestibular information. The nervous system undergoes through complex sensory and cognitive integration and continuous reassessment of the same in order to maintain balance. Present study investigated the cortical map changes in four different states of upright standing by means of calculating the EEG power spectral density distribution and its relation with postural sway. The prevailing role of the visual and proprioceptive input has been accentuated and the supra-spinal regulation of upright stance and balance were demonstrated by contemporary techniques. The results suggested that the prefrontal and parietal cortical areas play key role in solving the sensory conflicts. Keywords: EEG, postural sway, power spectral density, proprioceptive

INTRODUCTION Brain is the central processor for complete working and bodily movements. Walking and posture stability is a complex sensorymotor skill in that context.[1] The central nervous system plays an integral role in integrating the afferent information from the visual, somatosensory and vestibular systems and delivering the efferent signals.[2] Studies have ruled out the past assumption that postural stability is only under the control of subcortical structures i.e. cerebrum, brainstem and spinal cord.[3] Recent studies have presented the significant involvement of prefrontal cortex in postural regulation.[4] Since evolution transformed humans from being four legged species to two legged ones, the task of maintaining upright stance has become more cognitively demanding as well. Quiet standing involves the rhythmic change of centre of pressure due to postural sway. Also as the

environmental surroundings change incessantly in an unpredicted order, successful maintenance of stable posture requires periodic changes. For balance control during limb movement and postural sway, proprioceptive signal feedback from foot-sole is used by central nervous system.[5] Most effective measurements involve the characterization of centre of foot pressure (COFP) and body centre of mass (BCM) during standing or walking while studying the symmetry in force distribution.It has been observed that visual and sensory feedback reflects sensitive changes in parietal and premotor regions of the brain, [6] respectively. Due to this cortical contribution, postural stability measures have been suggested as a rehabilitation assessment tool for lower limb,[7â&#x20AC;&#x201C;9] as well as neural disabilities.[8] Upright stance management is however a complex task

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International Journal of Computational Biology and Bioinformatics

Vol. 2: Issue 2

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In Silico Single Nucleotide Polymorphism Analysis in Human Glutamate Dehydrogenase 1

Usra Latief1, Vivek Dhar Dwivedi2*

Department of Zoology, Uttaranchal College of Science and Technology, Dehradun, India Faculty of Science and Environment, Mahatma Gandhi Chitrakoot Gramodaya Vishwavidyalaya, Chitrakoot, Satna, Madhya Pradesh, India

ABSTRACT In the present study, various in silico analysis tools were used to analyze the structural and functional effect of non-synonymous or amino acid-changing single nucleotide polymorphisms (nsSNPs) in the human glutamate dehydrogenase (GDH) protein associated with HI/HA syndrome. Total 16 nsSNPs data were collected from various published literatures and analyzed to identify high-risk nsSNPs by evolutionary conservation analysis using ConSurf server. I-Mutant tool was used to examine whether these high-risk nsSNPs alter the structural stability of GDH protein. I-Mutant result revealed that each high-risk nsSNPs except N410 and S445 decreases the stability of GDH protein. In addition, ConSurf identified a number of other conserved residues and short patterns that may be structurally and functionally relevant. A 37 amino acid long conserved motif from 370 to 406 was also identified having 15 highly conserved and buried residues and 7 highly conserved and exposed residues. This study is very extensive in silico analysis of HI/HA syndrome associated mutations in the human GDH protein and can be a valuable for the better understanding of the effect of nsSNPs on structural stability of the human GDH. Keywords: GDH, HI/HA syndrome and mutation, nsSNP

INTRODUCTION The hyperinsulinism/hyperammonemia (HI/HA) syndrome has been recognized as the most prevalent form of inborn hyperinsulinism (HI) in which affected infants have both fasting and protein sensitive hypoglycemia together with continuously increased plasma ammonia levels.[1,2] A lasting increment in insulin secretion causes hyperinsulinism.[3–5] ATP/ADP ratio in B cells is responsible for the secretion of insulin. Glucose and leucine regulate insulin secretion by regulating glutaminolysis by glucose and by the direct action of glucose and leucine on glutamate dehydrogenase (GDH).[6,7] GDH is an enzyme found in the mitochondria of the cell.[8–12] GDH oxidizes glutamate to α-ketoglutarate using

a cofactor, NAD and/or NADP. It has been reported that the HI/HA syndrome is the cause of diffuse and moderate [13–16] hyperinsulinism. In this syndrome, GDH activity is increased due to its decreased sensitivity to allosteric inhibition by guanosine triphosphate (GTP). The regulatory mutations in the GDH enzyme, encoded by GLUD1 gene, were found to be responsible for the HI/HA syndrome.[17] The cytogenetic location of GLUD1 gene was mapped to 10q23.3. It is about 45 kb long and contains 13 exons coding for a 505-amino acid mature enzyme.[18,19] The human

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International Journal of Computational Biology and Bioinformatics

Vol. 2: Issue 2

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Effect of Gender and Performance on EMG Activity of Selected Knee Extensor Muscles during Isometric Contractions of Fully Extended Knee in Athletes Manvinder Kaur1, Sanjeev Nara1, Sateesh Reddy Avutu2, Dinesh Bhatia2*, Dhananjoy Shaw3 1

Department of Biomedical Engineering, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Haryana, India 2 Biomedical Engineering Department, North Eastern Hill University (NEHU), Shillong, Meghalaya, India 3 Indira Gandhi Institute of Physical Education and Sports Sciences, University of Delhi, Delhi, India

ABSTRACT Muscular fatigue is described as a condition, wherein the ability of muscles to contract and produce force is reduced under sustained contraction. The quantification of muscular fatigue by surface electromyography (EMG) provides a non-invasive method for easily accessing and measuring the physiological processes occurring during sustained muscular work. The isometric contraction consisted of performing knee extension with an angle between 180º and 170º with a load of 30 repetition maximum (RM) on the CYBEX exerciser. Vastus Medialis (VM) and Vastus Lateralis (VL) leg muscles were chosen for recording the EMG activity simultaneously. Statistical analysis showed significant differences between the gender as well as performance (high and low) in these athletes. EMG activity of males was found to be superior to females across the experimental protocol. Keywords: electromyography, fatigue, gender, isometric, performance

INTRODUCTION Muscular endurance is an inherent requirement of performing sport, especially high intensity sports such as (judo, weightlifting etc.). Also, endurance is related to the muscles acting about the knee joint rather than endurance of the knee joint. The muscular endurance of knee joint is considered to be one of the important factors in the competitive ability of an athlete.[1] In daily life, the knee joint is considered and established to be most prone to and suffering from different musculoskeletal injuries such as Anterior Cruciate ligament injuries, patella femoral joint injuries for both athletes and nonathletes as per the established literature.[1,2] Muscles of this joint should have high muscular endurance specifically of the athletic population for the maintenance of corporal stability and avoiding occurrence

of frequent injuries.[2] It is well documented in literature that muscle strength endurance represents one of the most important motor abilities in intense physical sporting activities.[3,4] Knee stabilization in any sporting task is important because knee serves as an important transmission between the ankle and hip joints.[5] Strengthening and balancing the muscles that surround the knee, helps in taking off the pressure around the knee joint and reduction in the amount of overall weight absorbed by the ligaments, meniscus and cartilage in the knee.[5,6] Isometric training exercises that involve the static contraction of the muscle are required for strengthening of the muscles and knee stability without the

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International Journal of Computational Biology and Bioinformatics

Vol. 2: Issue 2

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Analysis of Ground Reaction Force and Temporal Parameters during Human Gait for Design of Sensor Mechanism Ratan Das*, Devendra Mohan, Pallabi Baruah, Neelesh Kumar

Central Scientific Instruments Organization (CSIR-CSIO), Chandigarh, India

ABSTRACT Study and analysis of human ground reaction forces, spatial and temporal parameters forms an integral part of clinical gait analysis. Constrain stages keep on being the highest quality level for such estimations. This paper displays the investigations of various segments of ground response powers and stride stages utilizing active drive stages. Data for dynamic gait from different subjects were recorded and analyzed for measuring vertical ground reaction force during normal walk. A comparative analysis is also done for plotting variation of different spatio-temporal parameters during slow and normal speed. The objective of this study was to explore, understand and quantify the variation of gait parameters so that this information could be incorporated for effective design and development of portable gait analysis modules. Keywords: force plate, gait, ground reaction force, spatial parameter, temporal parameter

INTRODUCTION Human gait is a complex biomechanical process involving muscle actions. Ground reaction force (GRF) is developed during gait as a result of the force applied to the ground when the foot is in contact with it. Since GRF is external force acting on the body during locomotion, it is of great interest to gait analysis and can be used for validating the state of disorder of patients’ movement[1, 2]. When a foot is in contact with the ground, for example, vertical as well as shear (horizontal) forces are produced. The three components of GRF vector during gait are vertical force (Fz), anterior/posterior force (Fx), and medial/lateral force (FLy). Figure 1 shows

the typical nature of GRF during stance phase. The stride cycle is characterized as the time interim between two progressive events of one of the monotonous occasions of strolling [3]. Although any event could be considered to define the gait cycle, it is more convenient (and widely practiced) to use the instant at which one foot contacts the ground (‘initial contact’ or ‘heel strike’) as start of a new gait cycle. In the event that it is chosen to begin with heel strike of the right foot then the cycle will proceed until the right foot contacts the ground once more.

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International Journal of Computational Biology and Bioinformatics

Vol. 2: Issue 2

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A Review on Principles of Bioinformatics and Its Methods Based on Sequence Techniques Sona Singh*

Senior Project Officer, Indian Council of Food and Agriculture, New Delhi, India

ABSTRACT As it is evident, the genetic material is stored in DNA sequences and transcript in RNA and protein sequences, it makes sense to evaluate two or more biological sequences to look for resemblance and disparity that can be used to infer the relatedness of the sequences. These sequences are compared to generate information of their evolution with the help of latest technique of computational biology. Sequence alignment provides a way to arrange the sequences of genetic material to identify regions of similarity that may be an effect of functional, structural or evolutionary relationships between the sequences .This paper is focused on the perceptive of sequence based techniques and construction of algorithms that deal with problems of biological relevance that is widely known as computational biology or bioinformatics. It emphasize on utilizing the competence of computer to gain knowledge from biological data. The majority of issues in computational biology is linked to molecular and evolutionary biology and its focus is on analysis and comparison of the genetic material of organisms. One integral component in forming the outline of computational biology is DNA, RNA and protein. These elements are responsible for storing and utilizing the genetic material in an organism and can be described as strings over finite alphabets. Keywords: alignment, bioinformatics, sequence

INTRODUCTION Computational biology sometimes also known as bioinformatics is basically use of computational and statistical analysis to decode the biological information from genome sequences and data related to it. It concentrates on comprehension of the human genome and in general terms, emphasizes on the principles of how DNA controls the biology of any species at the molecular level. It includes both DNA and RNA sequence as well as other post-genomic data like experimental data obtained with technologies that require the genome sequence, such as genomic DNA microarrays. The best way to use computational genomics is to combine it with bioinformatics to explore new possibilities in the field of medicine. It utilizes algorithms and machine learning

procedures to find inconspicuous biological cipher in expansive genomes and uncover the instruments of genome advancement. The expedition of computational biology started in the mid-1960s (1965–1979) with hardbound Atlas of Protein Sequence and Structure [1–12]. In the United States, the National Center for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov/), a division of the National Library of Medicine (NLM), at the National Institute of Health (NIH), supports and distributes the GenBank nucleic acid sequence database,

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Office No-4, 1 Floor, CSC, Pocket-E, Mayur Vihar, Phase-2, New Delhi-110091, India E-mail: info@journalspub.com

20 mit icle b rt u S A Applied Mechanics r International Journal of Electro Mechanics and u Mechanical Behaviour International Journal of Machine Design and Yo Manufacturing

Mechanical Engineering

¬ International Journal of Thermal Energy and

¬ International Journal of Production Engineering ¬ International Journal of Industrial Engineering

« « «

Applications

International Journal of Mechanical Dynamics and Analysis International Journal of Fracture and damage Mechanics International Journal of Structural Mechanics and Finite Elements

and Design ¬ International Journal of Manufacturing and

Materials Processing ¬ International Journal of Mechanical Handling and

Automation 5 more...

Electronics and Telecommunication « International Journal of Radio Frequency Design « International Journal of VLSI Design and Technology « International Journal of Embedded Systems and Emerging

Technologies « International Journal of Digital Electronics « International Journal of Digital Communication and Analog

Chemical Engineering « International Journal of Renewable Energy and its

Commercialization « International Journal of Environmental Chemistry « International Journal of Agrochemistry « International Journal of Prevention and Control of Industrial

Pollution

5 more...

Signals

1 more...

Civil Engineering

Architecture « International Journal of Housing and Human Settlement

Planning « International Journal of Architecture and Infrastructure

Planning « International Journal of Rural and Regional Planning

« « « «

Development

« International Journal of Town Planning and Management

2 more...

Electrical Engineering

Computer Science and Engineering « « « « «

Nursing « « « « «

International Journal of Computational Biology & Bioinformatics IJCBB

Material Sciences and Engineering

« « « «

5 more...

Biotechnology « International Journal of Industrial Biotechnology and « « « «

Jul–Dec 2016

Nanotechnology « International Journal of Applied Nanotechnology « International Journal of Nanomaterials and Nanostructures « International Journals of Nanobiotechnology

Chemistry

Physics « International Journal of Solid State Materials « International Journal of Optical Sciences