| Description |
1 online resource |
| Contents |
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 |
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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 |
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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 |
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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 |
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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 |
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20 -- Next-generation alignment tools |
| Notes |
Print version record |
| Subject |
Bioinformatics.
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Computational biology.
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Computational Biology
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Bioinformatics
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Computational biology
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| Form |
Electronic book
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| Author |
Shafi, Afshana
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Masoodi, Khalid Z
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| ISBN |
9780323911290 |
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0323911293 |
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