Intro
Preface to Second Edition
Contents
List of Abbreviations
1: Introduction
1.1 Basics and History of Bioinformatics
1.1.1 Bioinformatics Is Integrating Many Scientific Fields
1.1.2 Homology
1.1.3 Evolution Is Related to Sequence Diversity Caused by Mutations
1.2 The Aim, Structure, and Outline of the Book
1.3 Computers and Operating Systems Required for Bioinformatics
1.4 Computer Programs and Pipelines
1.5 Activity
Further Reading
Basic bioinformatics text books
References
2: DNA Sequence Assembly and Annotation of Genes

2.1 DNA Sequencing
2.1.1 Sanger Sequencing
2.1.2 Massive Parallel, Short-Read Sequencing
2.1.2.1 Illumina (Sequencing by Synthesis)
2.1.3 DNA Sequencing in Metagenomic and for Single Cell Sequencing
2.1.4 Real-Time, Single Molecule Sequencing
2.1.4.1 PacBio®
2.1.4.2 Nanopore Sequencing
2.2 DNA Sequence Assembly
2.2.1 Base Calling and Trimming
2.2.2 Assembly of DNA Sequences
2.2.2.1 Assembly by Overlap Consensus Methods
2.2.2.2 Assembly by k-mer Strategy
2.2.2.3 Quality Criteria of the Final Assembled DNA Sequence

2.2.2.4 De Novo or with Reference
2.3 Closing of Genomes
2.4 DNA Sequence Formats
2.5 Annotation
2.5.1 Elements from Comparative Genomics Aiming Annotation
2.6 Activities
2.6.1 Annotation at RAST
Further Reading
References
3: Databases and Protein Structures
3.1 Introduction to Bioinformatics Databases
3.1.1 Data Formats Used with Bioinformatics Databases
3.2 Organization of Databases and Bioinformatics Institutions
3.3 Major Bioinformatics Databases
3.3.1 GenBank
3.3.2 The European Nucleotide Archive (ENA)
3.3.3 Swiss-Prot and UniProt

3.3.4 Genomics Databases
3.3.5 Raw Sequence Read Datasets
3.3.6 Other Databases
3.3.7 Primary and Secondary Bioinformatics Databases
3.3.8 Data Formats in Bioinformatics Databases
3.4 Accession Numbers
3.5 Protein Structure Databases and Predictions
3.5.1 Primary and Secondary Structures
3.5.2 Domain Prediction and Databases
3.5.2.1 Single Motif
3.5.2.2 Multiple Motifs
3.5.2.3 Full Domain
3.5.2.4 Mixing Different Methods
3.5.3 Protein 3D Structure
3.6 Overview of Proteomics Databases and Servers
3.7 Help to Databases
3.8 Activities

3.8.1 Download a Sequence from NCBI
3.8.2 Download a Genome from NCBI
3.8.3 Deposition of Sequence with GenBank
3.8.3.1 Procedure for Single DNA Sequences
3.8.3.2 Genomic Sequence
3.8.4 Protein Structure Prediction with Swiss Model and SPDBV
3.9 Example Illustrating Variable Information and Redundancy of a Primary Genomic Database and Comparison to Some Other Information in the Book
References
4: Pairwise Alignment, Multiple Alignment, and BLAST
4.1 The Pairwise Alignment Problem
4.1.1 Global or Local Pairwise Alignments?
4.1.2 Substitution Matrices