Bioinformatics for Everyone

Bioinformatics for Everyone provides a brief overview on currently used technologies in the field of bioinformatics—interpreted as the application of information science to biology— including various online and offline bioinformatics tools and softwares. The book presents valuable knowledge in a simplified way to help students and researchers easily apply bioinformatics tools and approaches to their research and lab routines. Several protocols and case studies that can be reproduced by readers to suit their needs are also included. Explains the most relevant bioinformatics tools available in a didactic manner so that readers can easily apply them to their research Includes several protocols that can be used in different types of research work or in lab routines Discusses upcoming technologies and their impact on biological/biomedical sciences Bioinformatics for Everyone Copyright Dedication 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 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 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 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 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 A B C D E F G H I J K L M N O P R S T U V W Z