Bioinformatics for Everyone

Front-Matter_2022_Bioinformatics-for-Everyone
	Bioinformatics for Everyone
Copyright_2022_Bioinformatics-for-Everyone
	Copyright
Dedication_2022_Bioinformatics-for-Everyone
	Dedication
Foreword_2022_Bioinformatics-for-Everyone
	Foreword
Preface_2022_Bioinformatics-for-Everyone
	Preface
Acknowledgement_2022_Bioinformatics-for-Everyone
	Acknowledgement
Chapter-1---Prologue-to-bioinformatics_2022_Bioinformatics-for-Everyone
	1. Prologue to bioinformatics
		1.1 Definition
		1.2 Concept of bioinformatics
		1.3 Advancements in bioinformatics
		1.4 Objectives of bioinformatics
		1.5 Components of bioinformatics
		1.6 Biological terminology
		1.7 The evolution of bioinformatics
		1.8 Applications
		1.9 Limitations
		1.10 Branches of bioinformatics
		Further reading
Chapter-2---Advances-in-DNA-sequencing_2022_Bioinformatics-for-Everyone
	2. Advances in DNA sequencing
		2.1 Introduction
		2.2 DNA sequencing process
		2.3 DNA sequencing in real time
		2.4 Maxam–Gilbert chemical cleavage method
		2.5 Sanger chain-termination method
		2.6 Automated fluorescence sequencing
		2.7 Next-generation DNA sequencing
		2.8 Sequence platform pros and cons
		2.9 Usage of DNA sequencing
		2.10 Challenges of DNA sequencing
		Further reading
Chapter-3---Bioinformatics-databases-and-tool_2022_Bioinformatics-for-Everyo
	3. Bioinformatics databases and tools
		3.1 List of databases
		3.2 Database query systems
		3.3 Genome databases
		3.4 List of genome databases
		3.5 Genome browsers and analysis platforms
		3.6 Genome database of model organisms
		3.7 Sequence databases
		3.8 DNA sequence databases
		3.9 Protein sequence databases
		3.10 Databases of protein domain
		3.11 Databases of protein family
		3.12 Databases of protein function
		3.13 Structure databases
		3.14 Protein structures database portals
		3.15 Protein structures – classification
		3.16 Protein structures – visualisation
		Further reading
Chapter-4---Nucleic-acid-sequence-databases_2022_Bioinformatics-for-Everyone
	4. Nucleic acid sequence databases
		4.1 Introduction
		4.2 Nucleic acid sequence databases
		4.3 EMBL
		4.4 EBI\'s mission
		4.5 The EMBL entry structure
		4.6 GenBank
		4.7 The GenBank entry structure
		4.8 Access to GenBank
		4.9 Protocol: retrieval of nucleotide sequence of a given gene from GenBank
		4.10 DDBJ
		4.11 Tasks of DDBJ
		4.12 Workflow of DDBJ
		4.13 The INSD
		4.14 Protein sequence databases
		4.15 Swiss-Prot
		4.16 PIR
		4.17 TrEMBL
		4.18 UniProt
		Further reading
Chapter-5---Pairwise-sequence-alignment_2022_Bioinformatics-for-Everyone
	5. Pairwise sequence alignment
		5.1 Definition
		5.2 Bio-significance
		5.3 Utility
		5.4 Developmental basis
		5.5 Evaluating the alignments
		5.6 Methods
		5.7 Global alignment
		5.8 Local alignment
		5.9 Algorithms for alignment
		5.10 Dot matrix method
		5.11 Dynamic programming method
		5.12 Dynamic programming for global alignment
		5.13 Dynamic programming for local alignment
		5.14 Some other programmes for pairwise sequence alignment
		Further reading
Chapter-6---Multiple-sequence-alignment_2022_Bioinformatics-for-Everyone
	6. Multiple sequence alignment
		6.1 Introduction
			6.1.1 What is multiple sequence alignment?
				6.1.1.1 Sequences
				6.1.1.2 Multiple sequence alignment
		6.2 Scoring
		6.3 Multiple sequence alignment – types
			6.3.1 Progressive Alignment Construction
				6.3.1.1 Advantages
				6.3.1.2 Disadvantages
			6.3.2 Iterative Alignment Construction
				6.3.2.1 Advantages
				6.3.2.2 Disadvantages
			6.3.3 Block-base alignment
		6.4 Methods for multiple sequence alignment
			6.4.1 Dynamic programming-based models
			6.4.2 Statistical methods and probabilistic models
		6.5 Usage of multiple sequence alignment
		6.6 Applications of multiple sequence alignment
		Further reading
Chapter-7---Multiple-sequence-alignment-tools---sof_2022_Bioinformatics-for-
	7. Multiple sequence alignment tools – software and resources
		7.1 Introduction
			7.1.1 Kalign
			7.1.2 MView
			7.1.3 WebPRANK
			7.1.4 TM-aligner
			7.1.5 Mustguseal (multiple structure-guided sequence alignment)
		7.2 How does mustguseal function?
			7.2.1 PSAweb
			7.2.2 PVS (protein variability server)
			7.2.3 PRALINE
			7.2.4 PROMALS3D
			7.2.5 MAFFT (CBRC)
		7.3 Some other MSA tools
			7.3.1 OPAL (progressive-iterative alignment)
			7.3.2 DIALIGN-TX
			7.3.3 CHAOS and DIALIGN web server
			7.3.4 UniProt align
			7.3.5 Phylo
			7.3.6 PRANK
			7.3.7 CRASP
			7.3.8 ProbCons
			7.3.9 DIALIGN
			7.3.10 Muscle (WS jabaws)
			7.3.11 R-Coffee
			7.3.12 PRANK API
			7.3.13 OD-seq
			7.3.14 BARCOD
			7.3.15 Edialign
			7.3.16 MAFCO
			7.3.17 MAFFT (REST)
			7.3.18 MSAprobs
			7.3.19 Clustal Omega (EBI)
			7.3.20 T-Coffee (EBI)
			7.3.21 Biojs-io-clustal
			7.3.22 PASTA
			7.3.23 SARA-Coffee
			7.3.24 Staccato
			7.3.25 MARS
			7.3.26 Malakite
			7.3.27 trimAl
			7.3.28 Multi-LAGAN
			7.3.29 Pro-Coffee
			7.3.30 R3D-2-MSA
			7.3.31 ProDA
			7.3.32 MSAProbs-MPI
			7.3.33 HmmCleaner
			7.3.34 MSA-PAD 2.0
			7.3.35 PnpProbs
			7.3.36 ANTICALIgN
			7.3.37 FAMSA
			7.3.38 KMAD
			7.3.39 VerAlign
		Further reading
Chapter-8---CLUSTALW-software_2022_Bioinformatics-for-Everyone
	8. CLUSTALW software
		8.1 ClustalW history
		8.2 ClustalW method
		8.3 Pros and cons of ClustalW
			8.3.1 Pros
			8.3.2 Cons
		8.4 ClustalW contribution to research
		8.5 Steps for retrieving multiple sequence alignment of mRNA sequences of various species using ClustalW
		Further reading
Chapter-9---Plant-genomic-data-and-resources-at_2022_Bioinformatics-for-Ever
	9. Plant genomic data and resources at NCBI
		9.1 Introduction
		9.2 Primary sequence data
		9.3 International sequence databases of nucleotides
		9.4 Trace archive
		9.5 Expressed Sequence Tags
		9.6 BAC end sequences
		9.7 Probe database
		9.8 Derived data/pre-calculated data
		9.9 UniGene clusters
		9.10 UniSTS
		9.11 Entrez Gene
		9.12 HomoloGene
		9.13 Conserved protein domains
		9.14 BLink
		9.15 Gene Expression Omnibus
		9.16 Plant-specific data resources
		9.17 PlantBLAST databases
		9.18 Genetic map data
		9.19 Methods for accessing the plant data at NCBI
		Further reading
Chapter-10---NCBI-BLAST_2022_Bioinformatics-for-Everyone
	10. NCBI BLAST
		10.1 Definition
		10.2 Introduction
		10.3 BLAST – alignments and scoring
		10.4 To compare BLAST search results
		10.5 Selecting a BLAST programme
		10.6 BLASTN (nucleotide BLAST)
		10.7 BLASTX
		10.8 BLASTP
		10.9 TBLASTN
		10.10 Tblastx
		10.11 Database selection
		10.12 Nucleotide-related databases
		10.13 Protein-related databases
		Reference
		Further reading
Chapter-11---BLAST--protocols_2022_Bioinformatics-for-Everyone
	11. BLAST: protocols
		11.1 Protocol 1: how to select a sequence using entrez
			11.1.1 Step by step method details
		11.2 Protocol 2: how to search for a nucleotide database using a nucleotide query: BLASTN
			11.2.1 Step by step method details
		11.3 Protocol 3: how to search a protein database using a translated nucleotide query: BLASTX
			11.3.1 Step by step method details
		11.4 Protocol 4: how to search a translated nucleotide database using a protein query: TBLASTN
			11.4.1 Step by step method details
		11.5 Protocol 5: how to compare two or more sequence
			11.5.1 Step by step method details
		11.6 Troubleshooting guide
		Further reading
Chapter-12---ExPASy-portal_2022_Bioinformatics-for-Everyone
	12. ExPASy portal
		12.1 Introduction
		12.2 History
		12.3 Resource of the SIB
		12.4 Databases available at ExPASy
		12.5 ExPASy tools for sequence analysis
		12.6 ExPASy proteomics tools
		12.7 Protocol: using ExPASy\'s ‘translate’ tool
		Further reading
Chapter-13---Primer-designing-tools_2022_Bioinformatics-for-Everyone
	13. Primer designing tools
		13.1 FastPCR
		13.2 AutoPrime
		13.3 MethPrimer
			13.3.1 Step by step method
		13.4 Oligo.Net
		13.5 GeneFisher
			13.5.1 AA – consensus backtranslation
			13.5.2 AA – codon table backtranslation
			13.5.3 DNA
			13.5.4 Primer calculation
		13.6 GenomePRIDE 1.0
			13.6.1 Features of GenomePRIDE
		13.7 CODEHOP
		13.8 Oligos 6.2
		13.9 Primo Pro 3.4
		13.10 Primo degenerate3.4
		13.11 RE-specific primer designing
		13.12 AlleleID
		13.13 Array Designer 2
			13.13.1 Standard array design
			13.13.2 Whole genome array
			13.13.3 Tiling arrays
		13.14 LAMP designer
		13.15 Beacon designer
		13.16 NetPrimer
		13.17 SimVector
		13.18 Primer Premier
		13.19 Web Primer
		13.20 Primer3
		13.21 The PCR suite
		Further reading
Chapter-14---Primer-designing-for-cloning_2022_Bioinformatics-for-Everyone
	14. Primer designing for cloning
		Further reading
Chapter-15---Restriction-analysis-tools_2022_Bioinformatics-for-Everyone
	15. Restriction analysis tools
		15.1 Introduction
		15.2 What is restriction mapping?
		15.3 Why is restriction mapping useful?
		15.4 Webcutter 2.0
			15.4.1 Step by step method
		15.5 WatCut
		15.6 Restriction enzyme picker
		15.7 Restriction Analyzer
			15.7.1 Step by step method
		15.8 Restriction Comparator
		15.9 Restriction enzyme digest of DNA
		15.10 RestrictionMapper
			15.10.1 Step by step methods
		15.11 Sequence extractor
		Further reading
Chapter-16---Restriction-analysis-using-NEBcut_2022_Bioinformatics-for-Every
	16. Restriction analysis using NEBcutter
		16.1 Step-by-step tutorial
		Further reading
Chapter-17---KEGG-database_2022_Bioinformatics-for-Everyone
	17. KEGG database
		17.1 Objectives
			17.1.1 Structure of the KEGG database
		17.2 KEGG DRUG
		17.3 KEGG BRITE
		17.4 KEGG GENOME
		17.5 KEGG GENES
		17.6 KEGG PATHWAY
		17.7 KEGG DISEASE
		17.8 KEGG PATHWAY database
			17.8.1 Applications
		17.9 Protocol 1: using KEGG database
		17.10 Protocol 2: using KEGG pathway database
		Further reading
Chapter-18---Database-for-annotation--visualisation-_2022_Bioinformatics-for
	18. Database for annotation, visualisation and integrated discovery
		18.1 Introduction
		18.2 Tools
		18.3 Functional annotation tool
		18.4 Gene functional classification tool
		18.5 Gene ID conversion tool
		18.6 Gene name viewer
		18.7 NIAID pathogen genome browser
		18.8 Terminology
			18.8.1 Annotation category
			18.8.2 Annotation source
			18.8.3 DAVID gene ID
			18.8.4 DAVID ID%
			18.8.5 DAVID knowledgebase
			18.8.6 EASE score
			18.8.7 Term
		18.9 DAVID file formats
		18.10 Functions
		18.11 Protocol
		Further reading
Chapter-19---Genome-analysis-browsers_2022_Bioinformatics-for-Everyone
	19. Genome analysis browsers
		19.1 Introduction
		19.2 Web-based genome browsers
		19.3 The university of California, Santa Cruz, genome browser
		19.4 Protocol
		19.5 ENSEMBL genome browser
		19.6 Protocol
		19.7 Standalone annotation browsers and editors
		19.8 Apollo
		19.9 The IGB
		19.10 Artemis
		Further reading
Chapter-20---Next-generation-alignment-tools_2022_Bioinformatics-for-Everyon
	20. Next-generation alignment tools
		20.1 Introduction
		20.2 Novoalign
		20.3 mrFAST/mrsFAST
		20.4 FANGS
		20.5 RMAP
		20.6 BWT
		20.7 Bowtie
		20.8 BWA
		20.9 SOAP2
		20.10 BFAST
		20.11 Next-generation sequencing alignment tools – websites
		Further reading
Chapter-21---Molecular-marker-storage-databases-and_2022_Bioinformatics-for-
	21. Molecular marker storage databases and data visualisation
		21.1 Introduction
		21.2 Marker storage databases
		21.3 dbSNP
		21.4 Using dbSNP
		21.5 HapMap
		21.6 IBISS
		21.7 Gramene
		21.8 Using GRAMENE
		21.9 Techniques for data visualisation
		21.10 Graphical map viewer
		Reference
		Further reading
Chapter-22---Introduction-to-computer-aided-dru_2022_Bioinformatics-for-Ever
	22. Introduction to computer-aided drug design
		22.1 CADD includes
		22.2 Databases
			22.2.1 PubChem
		22.3 DrugBank
		22.4 ZINC DB
		22.5 PDB
		22.6 ModBase
		22.7 File formats
			22.7.1 MDL molfile
			22.7.2 sdf
			22.7.3 PDB
		Further reading
Chapter-23---BioEdit-in-bioinformatics_2022_Bioinformatics-for-Everyone
	23. BioEdit in bioinformatics
		23.1 Features
		23.2 Protocol: sequence alignment using BioEdit
			23.2.1 Step by step tutorials
		23.3 Protocol: putting forward and reverse sequences together using BioEdit
		Further reading
Index_2022_Bioinformatics-for-Everyone
	Index
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		E
		F
		G
		H
		I
		J
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		L
		M
		N
		O
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		R
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		U
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