Bioinformatics for beginners : genes, genomes, molecular evolution, databases and analytical tools / by Supratim Choudhuri.

Includes bibliographical references and index.

Front Cover; Bioinformatics for beginners; Copyright Page; Contents; Preface; Acknowledgment; 1 Fundamentals of Genes and Genomes; 1.1 Biological Macromolecules, Genomics, and Bioinformatics; 1.2 DNA as the Universal Genetic Material; 1.3 DNA Double Helix; 1.3.1 Structural Units of DNA; 1.3.2 Linkage between Nucleotides; 1.3.3 Base-Pairing Rules, Double Helix, and Triple Helix; 1.3.4 Single-Stranded DNA; 1.3.5 Base Sequence and the Genetic Code; 1.4 Conformations of DNA; 1.5 Typical Eukaryotic Gene Structure; 1.5.1 Transcribed Region; 1.5.1.1 Intron-Splicing Signals.

1.5.1.2 Effect of Intron Phase on Alternative Splicing1.5.1.3 Evolution of Introns; 1.5.2 52 Flanking Region of Transcribed Genes; 1.5.3 32 Flanking Region of Transcribed Genes; 1.6 Mutations in the DNA Sequence; 1.7 Some Features of RNA; 1.7.1 Instability of mRNA; 1.7.2 52 and 32 Untranslated Regions of mRNA; 1.7.3 Secondary Structures in RNA; 1.8 Coding Versus Noncoding RNA; 1.8.1 Small Noncoding RNA, Long Noncoding RNA, Competing Endogenous RNA, and Circular RNA; 1.9 Protein Structure and Function; 1.9.1 Configuration and Chirality of Amino Acids; 1.9.2 Ionic Character of Amino Acids.

1.9.3 Relationship between Protein Function and the Location of Amino Acids in the Polypeptide Chain1.9.4 Linkage between Amino Acids-The Peptide Bond; 1.9.5 Four Levels of Protein Structure; 1.9.6 Acidic and Basic Proteins; 1.9.7 Nonstandard Amino Acids in Polypeptide Chains; 1.10 Genome Structure and Organization; 1.10.1 The Structure of a Representative Genome-The Human Genome; 1.10.2 Functional Sequence Elements in the Genome; 1.10.2.1 Promoters; 1.10.2.2 Enhancers; 1.10.2.3 Locus Control Regions; 1.10.2.4 Insulators.

1.10.3 Epigenetic Modifications of the Genome Can Edit the Language Written in the DNA Sequence and Add an Extra Layer of C ... 1.10.3.1 Histone Code; 1.10.3.2 The Dynamics of Epigenetic Changes; 1.10.4 Lessons Learned from the Second Phase of the ENCODE Project about the DNA Elements in the Human Genome and its Epige ... ; References; 2 Fundamentals of Molecular Evolution; 2.1 Bioinformatics, Molecular Evolution, and Phylogenetics; 2.2 Biological Evolution and Basic Premises of Darwinism; 2.2.1 First Experimental Demonstration of Evolutionary Principles in the Test Tube.

2.3 Molecular Basis of Heritable Genetic Variations-The Raw Materials for Evolution2.3.1 Molecular Basis of Mutation; 2.3.2 Recombination and Generation of Genetic Diversity; 2.3.3 Gene Flow and Introduction of Genetic Diversity; 2.3.4 Origin of New Genes, Creation of Genetic Diversity and Genome Evolution; 2.3.4.1 Origin of New Genes from Coding Sequences (Pre-existing Genes); 2.3.4.1.a Gene Duplication and the 2R Hypothesis; 2.3.4.1.b Exon Shuffling; 2.3.4.1.c Gene Fusion and Fission; 2.3.4.1.d Horizontal Gene Transfer; 2.3.4.2 Origin (de Novo) of New Genes from Noncoding Sequences.

Bioinformatics for Beginners provides a coherent and friendly treatment of bioinformatics for any student or scientist within biology who has not routinely performed bioinformatic analysis. The book discusses relevant principles needed to understand the theoretical underpinnings of bioinformatic analysis, and demonstrates with examples targeted analysis using freely available web-based software and publicly available databases. Eschewing non-essential information, the work focuses on principles and hands-on analysis and points to many further study options.

PDF (ScienceDirect, viewed on July 18, 2014).