Details

Basic Applied Bioinformatics


Basic Applied Bioinformatics


1. Aufl.

von: Chandra Sekhar Mukhopadhyay, Ratan Kumar Choudhary, Mir Asif Iquebal

112,99 €

Verlag: Wiley-Blackwell
Format: EPUB
Veröffentl.: 15.09.2017
ISBN/EAN: 9781119244417
Sprache: englisch
Anzahl Seiten: 472

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Beschreibungen

An accessible guide that introduces students in all areas of life sciences to bioinformatics Basic Applied Bioinformatics provides a practical guidance in bioinformatics and helps students to optimize parameters for data analysis and then to draw accurate conclusions from the results. In addition to parameter optimization, the text will also familiarize students with relevant terminology. Basic Applied Bioinformatics is written as an accessible guide for graduate students studying bioinformatics, biotechnology, and other related sub-disciplines of the life sciences. This accessible text outlines the basics of bioinformatics, including pertinent information such as downloading molecular sequences (nucleotide and protein) from databases; BLAST analyses; primer designing and its quality checking, multiple sequence alignment (global and local using freely available software); phylogenetic tree construction (using UPGMA, NJ, MP, ME, FM algorithm and MEGA7 suite), prediction of protein structures and genome annotation, RNASeq data analyses and identification of differentially expressed genes and similar advanced bioinformatics analyses. The authors Chandra Sekhar Mukhopadhyay, Ratan Kumar Choudhary, and Mir Asif Iquebal are noted experts in the field and have come together to provide an updated information on bioinformatics. Salient features of this book includes: Accessible and updated information on bioinformatics tools A practical step-by-step approach to molecular-data analyses Information pertinent to study a variety of disciplines including biotechnology, zoology, bioinformatics and other related fields Worked examples, glossary terms, problems and solutions Basic Applied Bioinformatics gives students studying bioinformatics, agricultural biotechnology, animal biotechnology, medical biotechnology, microbial biotechnology, and zoology an updated introduction to the growing field of bioinformatics.
Dedication Preface Acknowledgements List Of Abbreviations i. Molecular Sequences and Structures Page 1 Retrieval of Sequence(s) from NCBI Nucleotide DatabaseCS Mukhopadhyay; RK Choudhary 2 Retrieval of Protein Sequence from UniProtKBCS Mukhopadhyay; RK Choudhary 3 Downloading Protein StructureCS Mukhopadhyay; RK Choudhary 4 Visualizing Protein StructureCS Mukhopadhyay; RK Choudhary 5 Sequence Format ConversionCS Mukhopadhyay; RK Choudhary 6 Nucleotide Sequence Analysis using Sequence Manipulation Suite (SMS)CS Mukhopadhyay; RK Choudhary 7 Detection of  Restriction Enzyme SitesCS Mukhopadhyay; RK Choudhary ii. Sequence Alignment 8 Dot Plot AnalysisCS Mukhopadhyay; RK Choudhary 9 Needleman-Wunsch Algorithm (Global Alignment)CS Mukhopadhyay; RK Choudhary 10 Smith-Waterman Algorithm (Local Alignment)CS Mukhopadhyay; RK Choudhary 11 Sequence Alignment using Online ToolsCS Mukhopadhyay; RK Choudhary iii. Basic Local Alignment Search Tools 12 Basic Local Alignment Search Tool for nucleotide (BLASTn)CS Mukhopadhyay; RK Choudhary 13 Basic Local Alignment Search Tool for Amino Acid Sequences (BLASTp)CS Mukhopadhyay; RK Choudhary 14 BLASTxCS Mukhopadhyay; RK Choudhary 15 tBLASTnCS Mukhopadhyay; RK Choudhary 16 tBLASTxCS Mukhopadhyay; RK Choudhary iv. Primer Designing and Quality Checking 17 Primer Designing- BasicsCS Mukhopadhyay; RK Choudhary 18 Designing of PCR Primers using Primer3 Online ToolCS Mukhopadhyay; RK Choudhary 19 Quality Checking of the Designed PrimersCS Mukhopadhyay; RK Choudhary 20 Primer Designing for SYBR Green Chemistry of qPCRCS Mukhopadhyay; RK Choudhary v. Molecular Phylogenetics 21 Construction of Phylogenetic Tree: Unweighted Pair Group Method with Arithmetic mean (UPGMA)CS Mukhopadhyay; RK Choudhary 22 Construction of Phylogenetic tree: Fitch Margoliash (FM) AlgorithmCS Mukhopadhyay; RK Choudhary 23 Construction of Phylogenetic tree: Neighbor Joining MethodCS Mukhopadhyay; RK Choudhary 24 Construction of Phylogenetic Tree: Maximum Parsimony MethodCS Mukhopadhyay; RK Choudhary 25 Construction of Phylogenetic tree: Minimum Evolution MethodCS Mukhopadhyay; RK Choudhary 26 Construction of Phylogenetic Tree using MEGA7CS Mukhopadhyay; RK Choudhary 27 Interpretation of Phylogenetic TreesCS Mukhopadhyay; RK Choudhary vi. Protein Structure Prediction 28 Prediction of Secondary Structure of ProteinCS Mukhopadhyay; RK Choudhary 29 Prediction of Tertiary Structure of Protein: Sequence HomologyCS Mukhopadhyay; RK Choudhary 30 Protein Structure Prediction using Threading MethodCS Mukhopadhyay; HK Manku 31 Prediction of Tertiary Structure of Protein: Ab Initio ApproachCS Mukhopadhyay; RK Choudhary 32 Validation of Predicted Tertiary Structure ProteinCS Mukhopadhyay; RK Choudhary vii. Molecular Docking and Binding Site Prediction 33 Predicting Transcription Binding SitesS Jain; S Panwar; A Kumar 34 Predicting Translation Initiation SitesS Jain; S Panwar; A Kumar 35 Docking of Ligand ReceptorsCS Mukhopadhyay; HK Manku viii. Genome Annotation 36 Genome Annotation in ProkaryotesCS Mukhopadhyay; RK Choudhary 37 Genome Annotation in EukaryotesCS Mukhopadhyay; RK Choudhary ix. Advanced Biocomputational Analyses 38 Concepts of Real Time PCR Data AnalysisRK Choudhary 39 Overview of Micro-array Data AnalysisRK Choudhary 40 Single Nucleotide Polymorphism (SNP) Mining ToolsMA Iquebal; Sarika; D Kumar 41 In silico Mining of Simple Sequence Repeats (SSR) MarkersMA Iquebal; Sarika; D Kumar 42 Basics of RNA-Seq Data AnalysisGVPPSR Kumar; AP Sahoo; A Kumar 43 Functional Annotation of Common Differentially Expressed GenesGVPPSR Kumar; AP Sahoo; A Kumar 44 Identification of Differentially Expressed Genes (DEGs)GVPPSR Kumar; A Kumar; AP Sahoo 45 Estimating MicroRNA expression using miRDeep2 toolGVPPSR Kumar; A Kumar; AP Sahoo 46 In silico prediction of miRNA TargetsSarika; MA Iquebal; D Kumar x. Appendices App. A Usage of Internet for BioinformaticsRK Choudhary App. B Important Web-Resources for Bioinformatics Databases and ToolsCS Mukhopadhyay; RK Choudhary App. C Usage of NCBI Database ResourcesCS Mukhopadhyay; RK Choudhary App. D Usage of Important EMBL ToolsS Jain; S Panwar; A Kumar App. F Evolutionary Models of Molecular PhylogenyCS Mukhopadhyay; RK Choudhary  
About the Authors Chandra Sekhar Mukhopadhyay is an Assistant Scientist (Senior Scale) at the School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU) at Ludhiana, Punjab, India. Ratan Kumar Choudhary is an Assistant Professor at the School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU) at Ludhiana, Punjab, India. Mir Asif Iquebal is a Scientist at the Centre for Agricultural Bioinformatics, Indian Council of Agricultural Research-Indian Agricultural Statistics and Research Institute (ICAR-IASRI) at Pusa, New Delhi, India.
An Accessible Guide that Introduces Students in All Areas of Life Sciences to Bioinformatics Basic Applied Bioinformatics provides practical guidance in bioinformatics and helps students to optimize parameters for data analysis and then to draw accurate conclusions from the results. In addition to parameter optimization, the text will also familiarize students with relevant terminology. Basic Applied Bioinformatics is written as an accessible guide for graduate students studying bioinformatics, biotechnology, and other related sub-disciplines of the life sciences. This text outlines the basics of bioinformatics, including pertinent information such as downloading molecular sequences (nucleotide and protein) from databases; BLAST analyses; primer designing and its quality checking, multiple sequence alignment (global and local using freely available software); phylogenetic tree construction (using UPGMA, NJ, MP, ME, FM algorithm and MEGA7 suite), prediction of protein structures and genome annotation, RNASeq data analyses and identification of differentially expressed genes and similar advanced bioinformatics analyses. The authors, Chandra Sekhar Mukhopadhyay, Ratan Kumar Choudhary, and Mir Asif Iquebal are noted experts in the field and have come together to provide updated information on bioinformatics. Salient features of this book include: Accessible and updated information on bioinformatics tools A practical step-by-step approach to molecular-data analyses Information pertinent to study a variety of disciplines including biotechnology, zoology, bioinformatics and other related fields Worked examples, glossary terms, problems and solutions. Basic Applied Bioinformatics gives students studying bioinformatics, agricultural biotechnology, animal biotechnology, medical biotechnology, microbial biotechnology, and zoology an updated introduction to the growing field of bioinformatics.

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