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Basic applied bioinformatics

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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.

Author(s): Chandra Sekhar Mukhopadhyay, Ratan Kumar Choudhary, Mir Asif Iquebal
Publisher: John Wiley & Sons
Year: 2017

Language: English
Pages: xviii+451
City: Newark

""Title Page""
""Table of Contents""
""Preface""
""Acknowledgments""
""List of Abbreviations""
""SECTION I: Molecular Sequences and Structures""
""CHAPTER 1: Retrieval of Sequence(s) from the NCBI Nucleotide Database""
""1.1 INTRODUCTION""
""1.2 COMPONENTS OF THE NCBI NUCLEOTIDE DATABASE""
""1.3 OBJECTIVES""
""1.4 PROCEDURE""
""1.5 SOME USEFUL NUCLEOTIDE SEQUENCE DATABASES OF NCBI""
""1.6 QUESTIONS""
""CHAPTER 2: Retrieval of Protein Sequence from UniProtKB""
""2.1 INTRODUCTION""
""2.2 OBJECTIVE""
""2.3 PROCEDURE""
""2.4 QUESTIONS"" ""CHAPTER 3: Downloading Protein Structure""""3.1 INTRODUCTION""
""3.2 OBJECTIVE""
""3.3 PROCEDURE""
""3.4 QUESTIONS""
""CHAPTER 4: Visualizing Protein Structure""
""4.1 INTRODUCTION""
""4.2 OBJECTIVE""
""4.3 PROCEDURE""
""4.4 QUESTIONS""
""CHAPTER 5: Sequence Format Conversion""
""5.1 INTRODUCTION""
""5.2 OBJECTIVE""
""5.3 PROCEDURE""
""5.4 QUESTIONS""
""5.5 BRIEF DESCRIPTION OF SOME OF THE IMPORTANT MOLECULAR SEQUENCE FORMATS""
""CHAPTER 6: Nucleotide Sequence Analysis Using Sequence Manipulation Suite (SMS)""
""6.1 INTRODUCTION""
""6.2 OBJECTIVE""
""6.3 PROCEDURE"" ""6.4 FORMAT CONVERSION""""6.5 SEQUENCE ANALYSIS""
""6.6 SEQUENCE FIGURES""
""6.7 RANDOM SEQUENCES""
""6.8 MISCELLANEOUS""
""6.9 QUESTIONS""
""CHAPTER 7: Detection of Restriction Enzyme Sites""
""7.1 INTRODUCTION""
""7.2 OBJECTIVE""
""7.3 PROCEDURE (USING NEBCUTTER)""
""7.4 QUESTIONS""
""SECTION II: Sequence Alignment""
""CHAPTER 8: Dot Plot Analysis""
""8.1 INTRODUCTION""
""8.2 OBJECTIVE""
""8.3 PROCEDURE""
""8.4 PARAMETERS OF DOT PLOT ANALYSIS""
""8.5 INTERPRETATION""
""8.6 QUESTIONS""
""CHAPTER 9: Needlemanâ#x80
#x93
Wunsch Algorithm (Global Alignment)""
""9.1 INTRODUCTION"" ""9.2 OBJECTIVE""""9.3 PROCEDURE""
""9.4 QUESTIONS""
""CHAPTER 10: Smithâ#x80
#x93
Waterman Algorithm (Local Alignment)""
""10.1 INTRODUCTION""
""10.2 OBJECTIVE""
""10.3 PROCEDURE""
""10.4 QUESTIONS""
""CHAPTER 11: Sequence Alignment Using Online Tools""
""11.1 INTRODUCTION""
""11.2 OBJECTIVE""
""11.3 PROCEDURE""
""11.4 INTERPRETATION OF RESULTS""
""11.5 COLOR SCHEME FOR AMINO ACID RESIDUES""
""11.6 QUESTIONS""
""SECTION III: Basic Local Alignment Search Tools""
""CHAPTER 12: Basic Local Alignment Search Tool for Nucleotide (BLASTn)""
""12.1 INTRODUCTION""
""12.2 OBJECTIVE"" ""12.3 PROCEDURE""""12.4 QUESTIONS""
""CHAPTER 13: Basic Local Alignment Search Tool for Amino Acid Sequences (BLASTp)""
""13.1 INTRODUCTION""
""13.2 OBJECTIVE""
""13.3 PROCEDURE""
""13.4 QUESTIONS""
""CHAPTER 14: BLASTx""
""14.1 INTRODUCTION""
""14.2 OBJECTIVE""
""14.3 PROCEDURE""
""14.4 INTERPRETATION OF BLASTx RESULTS""
""14.5 QUESTIONS""
""CHAPTER 15: tBLASTn""
""15.1 INTRODUCTION""
""15.2 OBJECTIVE""
""15.3 PROCEDURE""
""15.4 ALGORITHM PARAMETERS""
""15.5 INTERPRETATION OF tBLASTn RESULTS""
""15.6 QUESTIONS""
""CHAPTER 16: tBLASTx""
""16.1 INTRODUCTION""