Kaynakça var.

CONTENTS Preface SECTION I. INTRODUCTION AND BIOLOGICAL DATABASES Chapter 1. Introduction What is bioinformatics The goal of bioinformatics The scope of bioinformatics Applications of bioinformatics Limitations of bioinformatics Future of bioinformatics Chapter 2. Introduction to Biological databases What is a database? Types of databases Relational databases Object-oriented databases Biological databases Primary databases Secondary databases Specialized databases Interconnection between biological databases Pitfalls of biological databases Database retrieval Entrez GenBank GenBank sequence format Alternative sequence formats FASTA ASN.1 Conversion of sequence formats SRS Summary Further Reading SECTION II. SEQUENCE ALIGNMENT Chapter 3. Pairwise Sequence Alignment Evolutionary basis of sequence alignment Sequence homology vs. sequence similarity Sequence similarity vs. sequence identity Methods of pairwise alignment Global alignment and local alignment Alignment algorithms Dot matrix method Dynamic programming method Gap penalties Dynamic programming for global alignment Dynamic programming for local alignment Scoring matrices Amino acid scoring matrices PAM marices BLOSUM matrices Comparision between PAM and BLOSUM DNA scoring matrices Statistical significance of sequence alignment Summary Further Reading Chapter 4. Database similarity search Unique requirement of database searching Heuristic database searching BLAST (Basic Local Alignment Search Tool) BLAST variants Statistical significance of BLAST results Filtering low complexity regions (LCRs) BLAST output format FASTA Comparison of FASTA and BLAST Database searching with the Smith-Waterman method Summary Further Reading Chapter 5. Multiple sequence alignment Scoring function Exhaustive multiple sequence alignment algorithms Heuristic multiple sequence alignment algorithms Progressive alignment method Drawbacks of progressive alignment and solutions Iterative alignment Consistency-based alignment Practical issues associated with multiple sequence alignment Alignment of protein-coding DNA sequences Alignment editing Alignment format conversion Summary Further Reading Chapter 6. Profiles and hidden Markov models Position specific scoring matrices Profiles PSI-BLAST Markov model Hidden Markov model Score computation in HMM Applications of HMM Summary Further Reading Chapter 7. Protein motifs and patterns Identification of motifs and domains in multiple sequence alignment Motif and domain databases using regular expressions Motif and domain databases using statistical models Caveats of protein motif and domain searches Protein family databases Motif discovery in unaligned sequences Expectation maximization Gibbs motif sampling Sequence logos Summary Further Reading SECTION III. GENE AND PROMOTER PREDICTION Chapter 8. Gene prediction Categories of gene prediction programs Gene prediction in prokaryotes Conventional determination of open reading frames Gene prediction using HMMs Performance evaluation Gene prediction in eukaryotes Eukaryotic gene prediction programs Ab initio based programs Homology based programs Consensus based programs Performance evaluation Summary Further Reading Chapter 9. Promoter and regulatory element prediction Promoter and regulatory elements in prokaryotes Promoter and regulatory elements in eukaryotes Prediction algorithms Ab initio based algorithms Prediction for prokaryotes Prediction for eukaryotes Phylogenetic footprintng based algorithms Profile based algorithms Summary Further Reading SECTION IV. MOLECULAR PHYLOGENETICS Chapter 10. Phylogenetics basics Molecular evolution and molecular phylogenetics Major assumptions in molecular phylogenetics Terminology related to phylogeny Gene phylogeny vs. species phylogeny Forms of tree representation Why finding a true tree is difficult? Procedure of phylogenetic analysis Choice of molecular markers Alignment for phylogenetic analysis Multiple substitutions Choosing substitution models Jukes-Cantor model Kimura model Among-site variation Summary Further Reading Chapter 11. Phylogenetic tree construction methods and programs Choosing tree-building methods Distance-based methods Clutering-based methods UPGMA Neighbor-joining Generalized NJ Optimality-based methods Fitch-Margoliash Minimum evolution Pros and Cons of distance methods Character-based methods Maximum parsimony method How does MP tree building work? Weighted parsimony Methods to search for tree topologies Pros and cons of parsimony methods Long branch attraction Maximum likelihood method How does the ML method work? Pros and cons of maximum likelihood method Quartet puzzling NJML Genetic algorithm Bayesian analysis Phylogenetic tree evaluation What is bootstrapping Parametric and nonparametric bootstrapping Caveats of bootstrapping Jackknifing Kishino-Hasegawa test Shimodaira-Hasegawa test Phylogenetic programs Summary Further Reading SECTION V. STRUCTURAL BIOINFORMATICS Chapter 12. Protein structure basics Amino acids Peptide formation Dihedral angles Ramachandran plot Hierarchy of protein structures Forces that stabilize protein structures Protein secondary structures Alpha helices Beta sheets Coiled coils Globular proteins Integral membrane proteins Determination of protein three dimensional structure X-ray crystallography NMR Protein structure database PDB format mmCIF and MMDB formats Summary Further Reading Chapter 13. Protein structure visualization, comparision and classification Protein structural visualization Protein structure comparison Intermolecular method to compare protein structures Intramolecular method to compare protein structures Combined method to compare protein structures Multiple structure alignment Protein structure classification SCOP CATH Comparison between SCOP and CATH Chapter 14. Protein secondary structure prediction Secondary structure prediction for globular proteins Ab-intio based methods Homology-based method Prediction with neural networks Prediction with multiple methods Comparison of prediction accuracy Secondary structure prediction for transmembrane proteins Prediction of helical membrane proteins Prediction of ?-barrel membrane proteins Coiled coil prediction Summary Further readings Chapter 15. Protein tertiary structure prediction Methods for protein structural prediction Homology Modeling Template selection Sequence alignment Backbone model building Loop modeling Side chain refinement Model optimization Model evaluation Comprehensive modeling programs Homology model databases Threading and fold recognition Pairwise energy method Profile method Ab initio protein structural prediction CASP Summary Further readings Chapter 16. RNA structure prediction Introduction to RNA structures Types of RNA structures RNA secondary structure prediction methods Ab initio approach Dot matrices Dynamic programming Partition function Comparative approach Algorithms that use pre-alignment Algorithms that do not use pre-alignment Performance evaluation Summary Further Reading SECTION VI. GENOMICS AND PROTEOMICS Chapter 17.

Genome mapping, assembly and comparison Genome mapping Genome sequencing Genome sequence assembly Base-calling and assembly programs Genome annotation Automated genome annotation Annotation of hypothetical proteins How many genes in a genome? Genome economy Genome comparison Whole genome alignment Finding a minimal genome Lateral gene transfer Identifying regions of genome with unusaual compositions Gene order comparison Summary Further Reading Chapter 18. Functional genomics Sequence-based approaches (ESTs and SAGE) Expressed Sequence Tags (ESTs) Organizing EST collections SAGE Microarry-based approaches Oligonucleotide design Data collection Image processing Data transformation and normalization Statistical analysis to identify differentially expressed genes Microarray data classification Distance measure Supervised and unsupervised classification Hierarchical clustering k-means clustering Self-organizing maps Clustering programs Comparison of SAGE and DNA microarrays Summary Further Reading Chapter 19. Proteomics Technology of proteome mapping 2D-PAGE Mass spectrometry protein identification Protein identification through database searching Differential in gel electrophoresis Protein microarrays Post-translational modification Prediction of disulfide bridges Identification of post-translational modification in proteomic analysis Protein sorting Protein-protein interactions Experimental determination Prediction of protein-protein interactions Predicting interactions based on domain fusion Predicting interactions based on gene neighbors Predicting interactions based on sequence homology Predicting interactions based on phylogenetic information Summary Further reading APPENDIX A.1 Practical Exercises A.2 Glossary INDEX