BookNoor Ahmad Shaik, Khalid Rehman Hakeem, Babajan Banaganapalli and Ramu Elango, editors.
Summary: Bioinformatics is an integrative field of computer science, genetics, genomics, proteomics, and statistics, which has undoubtedly revolutionized the study of biology and medicine in past decades. It mainly assists in modeling, predicting and interpreting large multidimensional biological data by utilizing advanced computational methods. Despite its enormous potential, bioinformatics is not widely integrated into the academic curriculum as most life science students and researchers are still not equipped with the necessary knowledge to take advantage of this powerful tool. Hence, the primary purpose of our book is to supplement this unmet need by providing an easily accessible platform for students and researchers starting their career in life sciences. This book aims to avoid sophisticated computational algorithms and programming. Instead, it mostly focuses on simple DIY analysis and interpretation of biological data with personal computers. Our belief is that once the beginners acquire these basic skillsets, they will be able to handle most of the bioinformatics tools for their research work and to better understand their experimental outcomes. Unlike other bioinformatics books which are mostly theoretical, this book provides practical examples for the readers on state-of-the-art open source tools to solve biological problems. Flow charts of experiments, graphical illustrations, and mock data are included for quick reference. Volume I is therefore an ideal companion for students and early stage professionals wishing to master this blooming field.
Contents:
Intro; Foreword; Preface; Contents; About the Editors;
Chapter 1: Introduction to Bioinformatics; 1.1 Introduction; 1.2 The Role of Bioinformatics in Gene Expression Data Analysis; 1.3 The Role of Bioinformatics in Gene/Genome Mapping; 1.4 Role of Bioinformatics in Sequence Alignment and Similarity Search; 1.5 Contribution of Bioinformatics toward Modern Cancer Research; 1.6 The Domain of Structural Bioinformatics; 1.7 Bioinformatics Processing of Big Data; 1.8 Conclusion; References;
Chapter 2: Introduction to Biological Databases; 2.1 Introduction to Databases; 2.2 Types of Databases 2.2.1 Relational Databases2.2.2 Object-Oriented Database; 2.3 Introduction to Biological Databases; 2.3.1 Classification of Biological Databases; 2.3.2 Primary Database; 2.3.3 Secondary Databases; 2.3.4 Specialized Databases; 2.3.5 Interconnection between Biological Databases; 2.4 Retrieval from Databases; 2.5 Conclusion; References;
Chapter 3: Sequence Databases; 3.1 Introduction; 3.2 Sequence Data Generation; 3.2.1 The First Generation of Sequencing; 3.2.2 The Second Generation of Sequencing; 3.2.3 The Third Generation of Sequencing; 3.3 Classes of Biological Databases 3.4 Types of Sequence Databases3.4.1 Nucleotide Sequence Databases; 3.4.1.1 EMBL/DDBJ/GenBank; 3.4.1.2 RefSeq; 3.4.1.3 Ensembl; 3.4.2 Protein Sequence Database; 3.4.2.1 TrEMBL; 3.4.2.2 GenPept; 3.4.2.3 Entrez Protein; 3.4.2.4 UniProt; 3.5 Sequence Submission; 3.5.1 Sequin; 3.5.2 BankIt; 3.5.3 Webin; 3.6 Retrieval; 3.6.1 SRS (Sequence Retrieval System); 3.6.2 Entrez; 3.6.3 DBGET; 3.7 Conclusion; References;
Chapter 4: Biological 3D Structural Databases; 4.1 Introduction; 4.1.1 X-Ray Crystallography; 4.1.2 Crystal Formation; 4.1.3 Structure Determination; 4.2 Macromolecular Structural Databases 4.2.1 Protein Data Bank wwPDB4.2.1.1 RCSB PDB; 4.3 PDBsum: Structural Summaries of PDB Entries; 4.4 sc-PDB: A 3D Database of Ligandable Binding Sites; 4.5 PDBTM: Protein Data Bank of Transmembrane Proteins; 4.6 CATH Database; 4.7 SCOP (Structural Classification of Proteins) Database; 4.8 Structure Comparison Servers; 4.9 Conclusion; References;
Chapter 5: Other Biological Databases; 5.1 Introduction; 5.2 Gene or Genome Annotation Databases; 5.2.1 GO/GOA Databases; 5.2.2 UCSC Genome Browser: Annotation Database; 5.3 Protein Annotation Databases; 5.3.1 PRIDE Archive; 5.3.2 SWISS-2DPAGE 5.3.3 Domain Databases5.4 Network Databases; 5.4.1 IntAct; 5.5 Pathway Databases; 5.5.1 Kyoto Encyclopedia of Genes and Genomes; 5.5.2 BioCyc; 5.5.3 Ingenuity Pathways Knowledge Base; 5.5.4 Reactome Pathway Databases; 5.5.5 Other Pathway Databases; 5.6 Drug Databases; 5.6.1 DrugBank; 5.6.2 PharmGKB; 5.6.3 ChEBI; 5.6.4 PubChem; 5.6.5 ZINC Database; 5.7 Specialized Database; 5.7.1 Model Organism Databases; 5.7.2 IntEnz; 5.7.3 EPD; 5.7.4 TRANSFAC; 5.8 Scientific Literature Database; 5.8.1 PubMed; 5.8.2 SCI (Science Citation Index); 5.8.3 Google Scholar; 5.9 Conclusion; References