BIF401 Handouts Set 2

Contents

Chapter 1Introduction to Bioinformatics ................................................................................................... 1 Module 001: INTRODUCTION TO BIOINFORMATICS ................................................................................ 1 Module 002: INTRODUCTION TO BIOINFORMATICS ................................................................................ 2 Module 003: INTRODUCTION TO BIOINFORMATICS ................................................................................ 3 Module 004: NEED FOR BIOINFORMATICS –II .......................................................................................... 4 Module 005: APPLICATIONS OF BIOINFORMATICS – I .............................................................................. 5 Module 006: APPLICATIONS OF BIOINFORMATICS - II ............................................................................. 6 Module 007: FRONTIERS IN BIOINFORMATICS - I ..................................................................................... 7 Module 008: FRONTIER IN BIOINFORMATICS-II ....................................................................................... 9 Module 009: Overview of Course Contents - I ........................................................................................ 10 Module 010: Overview of Course Contents - II ....................................................................................... 12 Module 011: Overview of Course Contents – III ..................................................................................... 15 Chapter 2 - Sequence Analysis .................................................................................................................... 18 Module 001: Gene, mRNA and Protein Sequences ................................................................................ 18 Module 002: TRANSCRIPTION ................................................................................................................. 20 Module 003: NUCLEOTIDES .................................................................................................................... 21 Module 004: TRANSLATION .................................................................................................................... 23 Module 005: AMINO ACIDS .................................................................................................................... 25 Module 006: STORAGE OF BIOLOGICAL SEQUENCE INFORMATION ...................................................... 27 Module 007: USING GENBANK ............................................................................................................... 28 Module 008: USING UNIPROT ................................................................................................................. 30 Module 009: COMPARING SEQUENCES .................................................................................................. 32 Module 010: SIMILARITIES & DIFFERENCES IN SEQUENCES ................................................................... 33 Module 011: SIMILARITIES & DIFFERENCES IN SEQUENCES ................................................................... 34 Module 012: PAIR WISE ALIGNMENT –II ................................................................................................ 35 Module 013: PAIR WISE SEQUENCE ALIGNMENT –III ............................................................................. 36 Module 014: DOT PLOTS ......................................................................................................................... 37 Module 015: EXEMPLE OF DOT PLOTS.................................................................................................... 39 Module 016: IDENTY VS SIMILARITY ....................................................................................................... 40 Module 017: INTRODUCTION TO ALIGNMENT APPROACHES ................................................................ 41 Module 018: WHY LOCAL ALIGNMENT ................................................................................................... 42 Module 019: ALIGNING, INSERTION & DELETION .................................................................................. 43 Module 020: ALIGNING MUTATION IN SEQUENCES ............................................................................... 44 Module 021: INTRODUCTION TO DYNAMIC PROGRAMMING ............................................................... 45 Module 022: DYNAMIC PROGRAMMING ESSENTIALS ............................................................................ 46 Module 023: DYNAMIC PROGRAMMING METHODOLOGY .................................................................... 47 Module 024: NEEDLEMAN WUNSCH ALGORITHM-I ............................................................................... 48 Module 025: NEEDLEMAN WUNSCH ALGORITHM-II .............................................................................. 50 Module 026: NEEDLEMAN WUNSCH ALGORITHM-III ............................................................................. 52 Module 027: NEEDLEMAN WUNSCH ALGORITHM EXAMPLE ................................................................. 53 Module 028: BACKTRACKING ALIGNMENTS ........................................................................................... 55 Module 029: REVISITING LOCAL AND GLOBAL ALIGNMENTS ................................................................. 56 Module 030: OVERLAP MATCHES ........................................................................................................... 57 Module 031: EXAMPLE ........................................................................................................................... 58 Module 032: MOVING FROM GLOBAL TO LOCAL ALIGNMENT .............................................................. 59 Module 033: SMITH WATERMAN ALGORITHM ...................................................................................... 60 Module 034: EXAMPLE OF SMITH WATERMAN ALGORITHM ................................................................ 61 Module 035: REPEATED ALIGNMENTS ................................................................................................... 62 Module 036: EXAMPLES OF REPEATED ALIGNMENTS ............................................................................ 63 Module 037: INTRODUCTION TO SCORING ALIGNMENTS ..................................................................... 64 Module 038: MEASURING ALIGNMENTS SCORES .................................................................................. 65 Module 039: SCORING MATRICES .......................................................................................................... 66 Module 040: DERIVING SCORING MATRICES .......................................................................................... 67 Module 041: PAM MATRICES.................................................................................................................. 69 Module 042: BLOSUM MATRICES ........................................................................................................... 70 Module 043: MULTIPLE SEQUENCE ALIGNMENT ................................................................................... 71 Module 044: MORE ON MULTIPLE SEQUENCE ALIGNMENT .................................................................. 72 Module 045: PROGRESSIVE ALIGNMENT FOR MSA ................................................................................ 74 Module 046: MSA-EXAMPLE ................................................................................................................... 76 Module 047: CLUSTALW ......................................................................................................................... 79 Module 048: INTRODUCTION TO BLAST-I ............................................................................................... 81 Module 049: INTRODUCTION TO BLAST-II .............................................................................................. 83 Module 050: BLAST ALGORITHM ............................................................................................................ 85 Module 051: TYPES OF BLAST ................................................................................................................. 86 Module 052: SUMMERY OF BLAST ......................................................................................................... 87 Module 053: INTRODUCTION TO FASTA ................................................................................................. 91 Module 054: INTRODUCTION TO FASTA-II ............................................................................................. 94 Module 055: FASTA ALGORITHM ............................................................................................................ 96 Module 056: TYPES OF FASTA ................................................................................................................. 98 Module 057: SUMMERY OF FASTA ......................................................................................................... 99 Module 058: BIOLOGICAL DATABASE AND ONLINE TOOLS .................................................................. 103 Module 059: EXPASY ............................................................................................................................. 104 Module 060: UNIPROT AND SWISSPROT .............................................................................................. 110 Module 061: PROTEIN DATA BANK ....................................................................................................... 112 Module 062: REVIEW OF SEQUENCE ALIGNMENT ............................................................................... 114 Module 063: GENBANK ......................................................................................................................... 115 Module 064: ENSEMBLE ....................................................................................................................... 116 Chapter 3 - Molecular Evolution ............................................................................................................... 117 Module 001: Molecular Evolution & Phylogeny ................................................................................... 117 Module 002: Evolution of Sequences ................................................................................................... 119 Module 003: Concepts and Terminologies - I ....................................................................................... 120 Module 004: Concepts and Terminologies - II ...................................................................................... 122 Module 005: Algorithms and Techniques ............................................................................................. 123 Module 006: Introduction to UPGMA ................................................................................................... 124 Module 007: UPGMA-I .......................................................................................................................... 126 Module 008: UPGMA-II ......................................................................................................................... 128 Module 009: UPGMA-III ........................................................................................................................ 131 Module 010: UPGMA-IV ........................................................................................................................ 133 Module 011: UPGMA-V ......................................................................................................................... 135 Chapter 4 - RNA Secondary Structure Prediction ..................................................................................... 137 Module 001: DNA TO RNA SEQUENCES ................................................................................................ 137 Module 002: TYPES OF RNA &THEIR FUNCTIONS ................................................................................. 138 Module 003: SIGNIFICANCES OF RNA STRUCTURE ............................................................................... 140 Module 004: RNA FOLDING AND ENERGY FOLDING ............................................................................ 142 Module 005: CALCULATING ENERGIES OF FOLDING-AN EXAMPLE ...................................................... 143 Module 006: TYPES OF RNA SECONDARY STRUCTURES-I ..................................................................... 144 Module 007: TYPES OF RNA SECONDARY STRUCTURES-II .................................................................... 146