Use of Bioinformatics Tools in Different Spheres of Life Sciences

Mehmood, Muhammad Aamer

doi:10.4172/2153-0602.1000158

Cited by 38 publications

(36 citation statements)

References 158 publications

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“…Even sequencing data for small virus was also very big and thus data handling was an issue for conducting these researches. This is where bioinformatics tool [26][27][28][29][30] helped in data management. Integrating these biological data with SQL and other programming languages helped a lot to support compilation and analysis of available data.…”

Section: Sequencing Data and Managementmentioning

confidence: 99%

A Review on New Horizons of Bioinformatics in Next Generation Sequencing, Viral and Cancer Genomics

Sharma¹

2016

Int J Biomed Data Min

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Genomics and molecular biology has always been a constant source of inspiration and motivational research for worldwide researchers in field of biology and biotechnology. These two fields have always generated a huge amount of data and in order to compile and analyze those, bioinformatics came into action during last decade. Implementation of bioinformatics has a clear intention of doing all these analysis of data in efficient and fast manner in order to cut down the expensive laboratory equipment, chemicals and most precious time. Mostly genomic data is composed of sequencing results at a higher scale and that is why manual curating and handling of these data is quite difficult. Supreme aim of this review is to make awareness about bioinformatics options in cancer genomics and viral genomics apart from next generation sequencing. Next generation sequencing or high throughput sequencing has helped a lot to replace old conventional method of sequencing and with the help of recent advances in technologies. These technologies are very efficient, fast and cheaper also as compare to conventional methods. Recently used methods were also discussed under appropriate headings. Role of bioinformatics is getting bigger and bigger in management and analysis of enormous amount of biological data generated through medical, biotechnological and clinical research globally. But we still need to understand challenges and limitation of bioinformatics as well as reliability.

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Section: Sequencing Data and Managementmentioning

confidence: 99%

A Review on New Horizons of Bioinformatics in Next Generation Sequencing, Viral and Cancer Genomics

Sharma¹

2016

Int J Biomed Data Min

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“…Over the past decades, powerful experimental approaches of computational biology have been largely raised from development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral and social systems (Ouzounis, 2012). Computational tools are routinely employed to test virtually hypotheses for characterization of genes, determining structural and physiochemical properties of proteins, phylogenetic analyses, and performing simulations to study how biomolecule interacts in a living cell (Mehmood et al, 2014). In silico studies of protein and nucleic acid is becoming a useful technique in the field of Bioinformatics, since the knowledge of the 3-D structure of a protein would be an invaluable aid to understand the details of a particular protein (Adzhubei et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

In silico prediction of the functional and structural consequences of the non-synonymous single nucleotide polymorphism A122V in bovine CXC chemokine receptor type 1

et al. 2020

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Abstract The current study aimed to assess whether the A122V causal polymorphism promotes alterations in the functional and structural proprieties of the CXC chemokine receptor type 1 protein (CXCR1) of cattle Bos taurus by in silico analyses. Two amino acid sequences of bovine CXCR1 was selected from database UniProtKB/Swiss-Prot: a) non-polymorphic sequence (A7KWG0) with alanine (A) at position 122, and b) polymorphic sequence harboring the A122V polymorphism, substituting alanine by valine (V) at same position. CXCR1 sequences were submitted as input to different Bioinformatics’ tools to examine the effects of this polymorphism on functional and structural stabilities, to predict eventual alterations in the 3-D structural modeling, and to estimate the quality and accuracy of the predictive models. The A122V polymorphism exerted tolerable and non-deleterious effects on the polymorphic CXCR1, and the predictive structural model for polymorphic CXCR1 revealed an alpha helix spatial structure typical of a receptor transmembrane polypeptide. Although higher variations in the distances between pairs of amino acid residues at target-positions are detected in the polymorphic CXCR1 protein, more than 97% of the amino acid residues in both models were located in favored and allowed conformational regions in Ramachandran plots. Evidences has supported that the A122V polymorphism in the CXCR1 protein is associated with increased clinical mastitis incidence in dairy cows. Thus, the findings described herein prove that the replacement of the alanine by valine amino acids provokes local conformational changes in the A122V-harboring CXCR1 protein, which could directly affect its post-translational folding mechanisms and biological functionality.

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“…Using docking analysis the targeted protein (esterase) and the ligand (Dichlorovos) was conducted to analyze the fitness and the interaction with each other in the form of energy. This interaction could be used as the pharmaceutical approach for drug production [9,10,11].…”

Section: Introductionmentioning

confidence: 99%

Studies on the Characterization of Esterase from Different Pisum sativum L. (Fabaceae) Varieties

Murthy¹,

Manjunath²,

Prakash³

et al. 2020

Rev. Chim.

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Pisum sativum L. (Fabaceae) is important in diet due to its fiber content, protein, starch, trace elements and phytochemical substances. Dichlorvos (2, 3-dichlorovinyl dimethyl phosphate) is commonly known as organophosphates belong to the classes of insecticides that are used to control households and stored products insects. The aim of this study was to analyze the kinetic characteristics of esterase enzyme from four different varieties of Pisum sativum L. using qualitative and quantitative method and also the docking position of esterase with Dichlorvos by insilico method. According to our study the total activity was highest for Arka Nirmala and Arka Priya varieties. The specific activity was highest for Arka Mayur variety. Km and Vmax, were found to be higher for Arka Uttam. The optimum temperature and pH for all the varieties were found to be same, 40�C and 7.5 respectively. The inhibitor studies showed Arka Nirmala was more sensitive to inhibitor. From the fitness and interaction profile it was found that the inhibitor dichlorovos is an effective pesticide which can be used to inhibit esterase activity. It has one hydrogen bond of H-S and had an amino acid residue at ARG57.

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Use of Bioinformatics Tools in Different Spheres of Life Sciences

Cited by 38 publications

References 158 publications

A Review on New Horizons of Bioinformatics in Next Generation Sequencing, Viral and Cancer Genomics

A Review on New Horizons of Bioinformatics in Next Generation Sequencing, Viral and Cancer Genomics

In silico prediction of the functional and structural consequences of the non-synonymous single nucleotide polymorphism A122V in bovine CXC chemokine receptor type 1

Studies on the Characterization of Esterase from Different Pisum sativum L. (Fabaceae) Varieties

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