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Bioinformatics for everyone /
| Clasificación: | Libro Electrónico |
|---|---|
| Autor principal: | |
| Otros Autores: | , |
| Formato: | Electrónico eBook |
| Idioma: | Inglés |
| Publicado: |
London :
Academic Press,
[2022]
|
| Temas: | |
| Acceso en línea: | Texto completo |
Tabla de Contenidos:
- Front Cover
- Bioinformatics for Everyone
- Bioinformatics for Everyone
- Copyright
- Dedication
- Contents
- Foreword
- Preface
- Acknowledgement
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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.
- 14
- Primer designing for cloning
- Further reading
- 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
- 16
- Restriction analysis using NEBcutter
- 16.1 Step-by-step tutorial
- Further reading
- 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
- 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
- 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.
- 20
- Next-generation alignment tools.