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Basic applied bioinformatics

Author: Chandra Sekhar Mukhopadhyay; Ratan Kumar Choudhary; Mir Asif Iquebal
Publisher: Hoboken, NJ, USA : Wiley Blackwell, 2018. ß2018
Edition/Format:   eBook : Document : EnglishView all editions and formats

"This book 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  Read more...


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Genre/Form: Electronic books
Additional Physical Format: Print version:
Material Type: Document, Internet resource
Document Type: Internet Resource, Computer File
All Authors / Contributors: Chandra Sekhar Mukhopadhyay; Ratan Kumar Choudhary; Mir Asif Iquebal
ISBN: 1119244374 9781119244370
OCLC Number: 1017716458
Description: 1 online resource (xvii, 451 pages, 34 unnumbered pages of plates) : illustrations (some color)
Contents: PREFACE, xiACKNOWLEDGEMENTS, xiiiLIST OF ABBREVIATIONS, xvSECTION I Molecular Sequences and Structures1 Retrieval of Sequence(s) from the NCBI Nucleotide Database, 32 Retrieval of Protein Sequence from UniProtKB, 93 Downloading Protein Structure, 154 Visualizing Protein Structure, 195 Sequence Format Conversion, 236 Nucleotide Sequence Analysis Using Sequence Manipulation Suite (SMS), 317 Detection of Restriction Enzyme Sites, 43SECTION II Sequence Alignment8 Dot Plot Analysis, 539 Needleman-Wunsch Algorithm (Global Alignment), 5910 Smith-Waterman Algorithm (Local Alignment), 6711 Sequence Alignment Using Online Tools, 73SECTION III Basic Local Alignment Search Tools12 Basic Local Alignment Search Tool for Nucleotide (BLASTn), 8113 Basic Local Alignment Search Tool for Amino Acid Sequences (BLASTp), 9114 BLASTx, 10315 tBLASTn, 10916 tBLASTx, 113SECTION IV Primer Designing and Quality Checking17 Primer Designing - Basics, 12118 Designing PCR Primers Using the Primer3 Online Tool, 12519 Quality Checking of the Designed Primers, 13920 Primer Designing for SYBR Green Chemistry of qPCR, 147SECTION V Molecular Phylogenetics21 Construction of Phylogenetic Tree: Unweighted?]Pair Group Method with Arithmetic Mean (UPGMA), 15122 Construction of Phylogenetic Tree: Fitch Margoliash (FM) Algorithm, 15923 Construction of Phylogenetic Tree: Neighbor?]Joining Method, 16524 Construction of Phylogenetic Tree: Maximum Parsimony Method, 17525 Construction of Phylogenetic Tree: Minimum Evolution Method, 18326 Construction of Phylogenetic Tree Using MEGA7, 18727 Interpretation of Phylogenetic Trees, 197SECTION VI Protein Structure Prediction28 Prediction of Secondary Structure of Protein, 21129 Prediction of Tertiary Structure of Protein: Sequence Homology, 21730 Protein Structure Prediction Using Threading Method, 22331 Prediction of Tertiary Structure of Protein: Ab Initio Approach, 22932 Validation of Predicted Tertiary Structure of Protein, 235SECTION VII Molecular Docking and Binding Site Prediction33 Prediction of Transcription Binding Sites, 24334 Prediction of Translation Initiation Sites, 25135 Molecular Docking, 257SECTION VIII Genome Annotation36 Genome Annotation in Prokaryotes, 26537 Genome Annotation in Eukaryotes, 269SECTION IX Advanced Biocomputational Analyses38 Concepts of Real?]Time PCR Data Analysis, 27539 Overview of Microarray Data Analysis, 28340 Single Nucleotide Polymorphism (SNP) Mining Tools, 28941 In Silico Mining of Simple Sequence Repeats (SSR) Markers, 29942 Basics of RNA?]Seq Data Analysis, 30543 Functional Annotation of Common Differentially Expressed Genes, 31344 Identification of Differentially Expressed Genes (DEGs), 32545 Estimating MicroRNA Expression Using the miRDeep2 Tool, 35746 miRNA Target Prediction, 365AppendicesAppendix A: Usage of Internet for Bioinformatics, 377Appendix B: Important Web Resources for Bioinformatics Databases and Tools, 381Appendix C: NCBI Database: A Brief Account, 389Appendix D: EMBL Databases and Tools: An Overview, 395Appendix E: Basics of Molecular Phylogeny, 403Appendix F: Evolutionary Models of Molecular Phylogeny, 411GLOSSARY, 415REFERENCES, 423WEBLIOGRAPHY, 431INDEX, 435
Responsibility: Chandra Sekhar Mukhopadhyay, Ratan Kumar Choudhary, Mir Asif Iquebal ; with contributions from Ravi GVPPS Kumar [and 8 others].


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