BIOINFORMATICS: A PRACTICAL GUIDE TO THE ANALYSIS OF GENES AND PROTEINS

By Y. KAIRL

CONTENTS 1 BIOINFORMATICS AND THE INTERNET INTERNET BASICS CONNECTING TO THE INTERNET ELECTRONIC MAIL FILE TRANSFER PROTOCOL THE WORLD WIDE WEB INTERNET RESOURCES FOR TOPICS PRESENTED IN CHAPTER REFERENCES 2 THE NCBI DATA MODEL INTRODUCTION PUBS: PUBLICATIONS OR PERISH SEQ-IDS: WHAT’S IN A NAME? BIOSEQS: SEQUENCES BIOSEQ-SETS: COLLECTIONS OF SEQUENCES SEQ-ANNOT: ANNOTATING THE SEQUENCE SEQ-DESCR: DESCRIBING THE SEQUENCE USING THE MODEL CONCLUSIONS 3 THE GENBANK SEQUENCE DATABASE PRIMARY AND SECONDARY DATABASES FORMAT VS CONTENT: COMPUTERS VS HUMANS THE DATABASE THE GENBANK FLAT?LE: A DISSECTION CONCLUDING REMARKS APPENDICES APPENDIX 3 1 EXAMPLE OF GENBANK FLAT?LE FORMAT APPENDIX 3 2 EXAMPLE OF EMBL FLAT?LE FORMAT APPENDIX 3 3 EXAMPLE OF A RECORD IN CON DIVISION 4 SUBMITTING DNA SEQUENCES TO THE DATABASES WHY, WHERE, AND WHAT TO SUBMIT? DNA/RNA POPULATION, PHYLOGENETIC, AND MUTATION STUDIES PROTEIN-ONLY SUBMISSIONS HOW TO SUBMIT ON THE WORLD WIDE WEB HOW TO SUBMIT WITH SEQUIN UPDATES CONSEQUENCES OF THE DATA MODEL EST/STS/GSS/HTG/SNP AND GENOME CENTERS CONTACT POINTS FOR SUBMISSION OF SEQUENCE DATA TO DDBJ/EMBL/GENBANK 5 STRUCTURE DATABASES INTRODUCTION TO STRUCTURES PDB: PROTEIN DATA BANK AT THE RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICS (RCSB) MMDB: MOLECULAR MODELING DATABASE AT NCBI STUCTURE FILE FORMATS VISUALIZING STRUCTURAL INFORMATION DATABASE STRUCTURE VIEWERS ADVANCED STRUCTURE MODELING STRUCTURE SIMILARITY SEARCHING PROBLEM SET 6 GENOMIC MAPPING AND MAPPING DATABASES INTERPLAY OF MAPPING AND SEQUENCING GENOMIC MAP ELEMENTS TYPES OF MAPS COMPLEXITIES AND PITFALLS OF MAPPING DATA REPOSITORIES MAPPING PROJECTS AND ASSOCIATED RESOURCES PRACTICAL USES OF MAPPING RESOURCES 7 INFORMATION RETRIEVAL FROM BIOLOGICAL DATABASES INTEGRATED INFORMATION RETRIEVAL: THE ENTREZ SYSTEM LOCUSLINK SEQUENCE DATABASES BEYOND NCBI MEDICAL DATABASES 8 SEQUENCE ALIGNMENT AND DATABASE SEARCHING THE EVOLUTIONARY BASIS OF SEQUENCE ALIGNMENT THE MODULAR NATURE OF PROTEINS OPTIMAL ALIGNMENT METHODS SUBSTITUTION SCORES AND GAP PENALTIES STATISTICAL SIGNI?CANCE OF ALIGNMENTS DATABASE SIMILARITY SEARCHING FASTA BLAST DATABASE SEARCHING ARTIFACTS POSITION-SPECI?C SCORING MATRICES SPLICED ALIGNMENTS 9 CREATION AND ANALYSIS OF PROTEIN MULTIPLE SEQUENCE ALIGNMENTS WHAT IS A MULTIPLE ALIGNMENT, AND WHY DO IT? STRUCTURAL ALIGNMENT OR EVOLUTIONARY ALIGNMENT? HOW TO MULTIPLY ALIGN SEQUENCES TOOLS TO ASSIST THE ANALYSIS OF MULTIPLE ALIGNMENTS COLLECTIONS OF MULTIPLE ALIGNMENTS 10 PREDICTIVE METHODS USING DNA SEQUENCES GRAIL FGENEH/FGENES MZEF GENSCAN PROCRUSTES HOW WELL DO THE METHODS WORK? STRATEGIES AND CONSIDERATIONS 11 PREDICTIVE METHODS USING PROTEIN SEQUENCES PROTEIN IDENTITY BASED ON COMPOSITION PHYSICAL PROPERTIES BASED ON SEQUENCE MOTIFS AND PATTERNS SECONDARY STRUCTURE AND FOLDING CLASSES SPECIALIZED STRUCTURES OR FEATURES TERTIARY STRUCTURE 12 EXPRESSED SEQUENCE TAGS (ESTS) WHAT IS AN EST? EST CLUSTERING TIGR GENE INDICES STACK ESTS AND GENE DISCOVERY THE HUMAN GENE MAP GENE PREDICTION IN GENOMIC DNA ESTS AND SEQUENCE POLYMORPHISMS ASSESSING LEVELS OF GENE EXPRESSION USING ESTS 13 SEQUENCE ASSEMBLY AND FINISHING METHODS THE USE OF BASE CELL ACCURACY ESTIMATES OR CON?DENCE VALUES THE REQUIREMENTS FOR ASSEMBLY SOFTWARE GLOBAL ASSEMBLY FILE FORMATS PREPARING READINGS FOR ASSEMBLY THE CONTIG SELECTOR THE CONTIG COMPARATOR THE TEMPLATE DISPLAY THE CONSISTENCY DISPLAY THE CONTIG EDITOR THE CONTIG JOINING EDITOR DISASSEMBLING READINGS EXPERIMENT SUGGESTION AND AUTOMATION 14 PHYLOGENETIC ANALYSIS FIONA S L BRINKMAN AND DETLEF D LEIPE FUNDAMENTAL ELEMENTS OF PHYLOGENETIC MODELS TREE INTERPRETATION—THE IMPORTANCE OF IDENTIFYING PARALOGS AND ORTHOLOGS PHYLOGENETIC DATA ANALYSIS: THE FOUR STEPS ALIGNMENT: BUILDING THE DATA MODEL ALIGNMENT: EXTRACTION OF A PHYLOGENETIC DATA SET DETERMINING THE SUBSTITUTION MODEL TREE-BUILDING METHODS DISTANCE, PARSIMONY, AND MAXIMUM LIKELIHOOD: WHAT’S THE DIFFERENCE? TREE EVALUATION PHYLOGENETICS SOFTWARE INTERNET-ACCESSIBLE PHYLOGENETIC ANALYSIS SOFTWARE SOME SIMPLE PRACTICAL CONSIDERATIONS 15 COMPARATIVE GENOME ANALYSIS MICHAEL Y GALPERIN AND EUGENE V KOONIN PROGRESS IN GENOME SEQUENCING GENOME ANALYSIS AND ANNOTATION APPLICATION OF COMPARATIVE GENOMICS—RECONSTRUCTION OF METABOLIC PATHWAYS AVOIDING COMMON PROBLEMS IN GENOME ANNOTATION PROBLEMS FOR ADDITIONAL STUDY 16 LARGE-SCALE GENOME ANALYSIS TECHNOLOGIES FOR LARGE-SCALE GENE EXPRESSION COMPUTATIONAL TOOLS FOR EXPRESSION ANALYSIS HIERARCHICAL CLUSTERING PROSPECTS FOR THE FUTURE 17 USING PERL TO FACILITATE BIOLOGICAL ANALYSIS LINCOLN D STEIN GETTING STARTED HOW SCRIPTS WORK STRINGS, NUMBERS, AND VARIABLES ARITHMETIC VARIABLE INTERPOLATION BASIC INPUT AND OUTPUT FILEHANDLES MAKING DECISIONS CONDITIONAL BLOCKS WHAT IS TRUTH? LOOPS COMBINING LOOPS WITH INPUT STANDARD INPUT AND OUTPUT FINDING THE LENGTH OF A SEQUENCE FILE PATTERN MATCHING EXTRACTING PATTERNS ARRAYS ARRAYS AND LISTS SPLIT AND JOIN HASHES A REAL-WORLD EXAMPLE WHERE TO GO FROM HERE SUGGESTED READING