Efnisyfirlit

• Cover
• Half-Title Page
• Series Page
• Title Page
• Copyright Page
• Table of Contents
• Acknowledgments
• Preface
• Author bio
• Chapter 1 The Origin of Genomic Information
• Introduction
• Genetic Information and Its Transmission
• Structure of DNA and Genome
• Gene Structure
• Gene Regulatory Region
• Introns
• Exons
• The Non-Coding Genomic Sequences
• Repetitive Sequences
• Pseudogenes
• Telomeres
• Ribonucleic Acid
• Ribosomal RNA
• Transfer RNA
• MicroRNA
• Messenger RNA
• Messenger RNA transcription
• Messenger RNA Translation
• The Proteins
• Three-Dimensional Protein Structure
• Protein Structure Representation and File Formats
• PDB File Format
• PDBx or mmCIF File Format
• Visualizing Protein Structure
• Gene Mutations
• Virus Genome
• References
• Chapter 2 The Sources of Genomic Data
• Introduction
• Extraction of DNA, RNA, and Proteins
• DNA, RNA, and Protein Quality
• Reverse Transcription
• Polymerase Chain Reaction
• First-Generation Sequencing
• Maxam-Gilbert Sequencing
• Sanger Chain-Terminator Sequencing Method
• Sanger Dye-Terminator Sequencing Method
• Next-Generation Sequencing
• Library Preparation
• TruSeq-style DNA Preparation
• Nextera DNA Preparation
• Enrichment Strategy
• RNA-Sequencing Library Preparation
• Multiplexing and Use of Barcodes
• Sequencing by Synthesis
• Single-end read sequencing
• Paired-end sequencing
• Mate Pair Sequencing
• Base Calling, Base Quality Score, and FASTQ File Format
• Base Calling and Base Quality Score
• FASTQ File Format
• Downstream NGS Data Analysis
• References
• Chapter 3 The NCBI Entrez Databases
• Introduction
• Entrez Retrieval Web Interface
• Entrez Database Web Page
• Entrez Database Indexed Fields
• Searching Entrez Databases
• Entrez Search Results
• Nucleotide Database
• Submission of Sequence Data to GenBank
• GenBank Format
• Nucleotide Sub Databases
• Expressed Sequence Tags
• Genome Survey Sequences
• Sequence-Tagged Sites
• Reference Sequence
• RefSeqGene
• Searching Nucleotide Database
• General Nucleotide Searching Strategy
• Worked Examples
• Gene Database
• Biocollections
• Protein Databases
• Protein Database
• Protein Clusters
• Identical Protein Groups
• Conserved Domain Database
• Finding Conserved Domain of Proteins
• Finding Protein Conserved Domains Using CD-Search
• Finding Proteins with Similar Domain Architectures
• Protein Family Models
• Introduction to Protein Classification
• Protein Family Models Database
• Annotation of Prokaryotic Genome
• HomoloGene
• BioProject
• BioSample
• dbSNP
• The dbSNP Submission
• Searching the dbSNP Database
• dbSNP Record Page
• dbVar Database
• Submission to dbVar Database
• Structural Variant Representation
• Searching dbVar
• The dbVar Record Page
• ClinVar Database
• Submitting Data to ClinVar
• Searching ClinVar Database
• ClinVar Record Page
• Gene Expression Omnibus (GEO) Database
• Submitting Gene Expression Data to GEO
• GEO DataSets
• GEO DataSets Searching Examples
• GEO Profiles
• Searching GEO Profiles
• Assembly
• Assembly Submission
• Searching the Assembly Database
• Genome Database
• Searching Genome Database
• Browse by Organism
• Human Genome
• Genome Data Viewer
• Genome Data Viewer Front Page
• Components of Genome Data Viewer
• Using Tools Menu
• Using Tracks Menu
• 100 Genome Browser
• Online Mendelian Inheritance in Man
• Searching OMIM
• Searching OMIM from Entrez Interface
• Searching OMIM from Original OMIM Interface
• OMIM Gene Record Page
• OMIM Phenotype Record Page
• PopSet
• Searching PopSet Database
• BioSystems
• Searching BioSystems
• Finding Genes and Proteins Involved in a Pathway
• Finding a Pathway by a Gene
• dbGaP
• Submitting Data to dbGaP
• Accessing dbGaP Data
• Searching dbGaP
• SRA Database
• Submitting Data to SRA Database
• Searching for SRA Data
• Installing SRA Toolkit
• Using SRA Toolkit Executables
• Downloading SRA Files with Prefetch
• Extracting Data from SRA Files
• Extracting Data from dbGaP Non-SRA Files
• Validation of Downloaded SRA Data Integrity
• Taxonomy
• NCBI Literature Databases
• PubMed
• Searching PubMed Database
• PubMed Record Page
• MeSH
• PubMed Central
• Bookshelf
• References
• Chapter 4 NCBI Entrez E-Utilities and Applications
• Introduction
• NCBI Application Programming Interface Key
• NCBI History Server
• E-utilities Programs
• EInfo
• Gquery
• ESearch
• EPost
• ESummary
• EFetch
• ELink
• ESpell
• ECitMatch
• References
• Chapter 5 The Entrez Direct
• Introduction
• EDirect Installation
• Installing EDirect on Linux and MacOS
• Installing EDirect on Windows 10
• Using EDirect
• EInfo
• ESearch
• EFetch
• ELink
• EFilter
• Epost
• Nquire
• Xtract
• XML Structure of Entrez Database Records and Data Types
• Identifying Patterns and Elements in an XML Document
• Extracting XML Child Elements
• Extracting XML Attribute
• Formatting Columns
• Grouping of Child Elements by Parents
• Using Xtract Conditional Arguments with Elements
• Using Xtract Conditional Arguments with String Constraints
• Extracting Data from Docsum Format
• Extracting Data from INSDSeq Format
• Extending EDirect with Bash Shell Script
• References
• Chapter 6 R and Python Packages for the NCBI E-Utilities
• Introduction
• R Entrez Package
• List the NCB Databases
• Displaying a Database Summary
• Displaying the Field List of a Database
• Searching Entrez Databases
• Getting Summary Data from Records
• Extracting Summary Data from Records
• Fetching Database Records
• Listing Linked Databases and Records
• Using BioPython for Entrez Databases
• Installing Python
• Installing Python and BioPython on Linux
• Installing Python and BioPython on Windows
• Using BioPython Entrez Package
• Getting Information of Entrez Databases
• Searching Entrez Databases
• Uploading UIDs to the History Server
• Retrieving Records’ Summaries
• Fetching Data from Entrez Database Records
• Finding Related Records in NCBI Databases
• Printing Records Counts of All Entrez Databases
• Providing Correction Suggestions
• References
• Chapter 7 Pairwise Sequence Alignment
• Introduction
• Pairwise Sequence Alignment
• Global Sequence Alignment
• Similarity Scores
• Global Alignment Algorithm
• Local Sequence Alignment and Algorithm
• BLAST Algorithm
• PSI-BLAST
• References
• Chapter 8 Basic Local Alignment Search Tool
• Introduction
• Web BLAST
• BLAST Field Description
• Using BLAST
• Aligning Two Sequences
• Aligning Multiple Sequences
• Identifying a Nucleotide Sequence
• Finding Closely Related Species
• Identifying Unknown Bacteria Using 16S rRNA Sequence
• Constructing Phylogenetic Tree for Human Related Species
• Constructing Phylogenetic Tree Using Protein Sequences
• Annotate a Metagenomic Contig
• Finding Protein Conserved Domains with Solved Structures
• Designing Primers for PCR
• Stand-Alone BLAST
• Installing and Running local BLAST on Windows
• Installing and Running Local BLAST on Linux
• Building a BLAST Database
• The Use of the Local BLAST
• References
• Index