Basic applied bioinformatics /

"An accessible guide that introduces students in all areas of life sciences to bioinformatics Basic Applied Bioinformatics provides a practical guidance in bioinformatics and helps students to optimize parameters for data analysis and then to draw accurate conclusions from the results. In addit...

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Detalles Bibliográficos
Clasificación:Libro Electrónico
Autores principales: Mukhopadhyay, Chandra Sekhar (Autor), Choudhary, Ratan Kumar (Autor), Iquebal, Mir Asif (Autor)
Formato: Electrónico eBook
Idioma:Inglés
Publicado: Hoboken, NJ : John Wiley & Sons, Inc., 2018.
Temas:
Bioinformatics > Textbooks.
Bioinformatics.
Computational biology.
Computational Biology
Bio-informatique.
MEDICAL > Biostatistics.
SCIENCE > Life Sciences > Biochemistry.
Textbook
Textbooks.
Acceso en línea:Texto completo (Requiere registro previo con correo institucional)
Tabla de Contenidos:
  • Section I: Molecular sequences and structures. Retrieval of sequence(s) from the NCBI Nucleotide database
  • Retrieval of protein sequence from UniProtKB
  • Downloading protein structure
  • Visualizing protein structure
  • Sequence format conversion
  • Nucleotide sequence analysis using sequence manipulation suite (SMS)
  • Detection of restriction enzyme sites
  • Section II: Sequence alignment. dot plot analysis
  • Needleman-Wunsch algorithm (global alignment)
  • Smith-Waterman algorithm (local alignment)
  • Sequence alignment using online tools
  • Section III: Basic local alignment search tools. Basic local alignment search tool for Nucleotide (BLASTn)
  • Basic local alignment search tool for amino acid sequences (BLASTp)
  • BLASTx
  • tBLASTn
  • tBLASTx
  • Section IV: Primer designing and quality checking. Primer designing: basics
  • Designing PCR primers using the Primer3 online tool
  • Quality checking of the designed primers
  • Primer designing for SYBR green chemistry of qPCR
  • Section V: Molecular phylogenetics. Construction of phylogenetic tree: unweighted-pair group method with arithmetic mean (UPGMA)
  • Construction of phylogenetic tree: Fitch Margoliash (FM) algorithm
  • Construction of phylogenetic tree: neighbor-joining method
  • Construction of phylogenetic tree: maximum parsimony method
  • Construction of phylogenetic tree: minimum evolution method
  • Construction of phylogenetic tree using MEGA7
  • Interpretation of phylogenetic trees
  • Section VI: Protein structure prediction. Prediction of secondary structure of protein
  • Prediction of tertiary structure of protein: sequence homology
  • Protein structure prediction using threading method
  • Prediction of tertiary structure of protein: ab initio approach
  • Validation of predicted tertiary structure of protein
  • Section VII: Molecular docking and binding site prediction. Prediction of transcription binding sites
  • Prediction of translation initiation sites
  • Molecular docking
  • Section VIII: Genome annotation. Genome annotation in prokaryotes
  • Genome annotation in eukaryotes
  • Section IX: Advanced biocomputational analyses. Concepts of real-time PCR data analysis
  • Overview of microarray data analysis
  • Single nucleotide polymorphism (SNP) mining tools
  • In silico mining of simple sequence repeats (SSR) markers
  • Basics of RNA-seq data analysis
  • Functional annotation of common differentially expressed genes
  • Identification of differentially expressed genes (DEGs)
  • Estimating MicroRNA expression using the miRDeep2 tool
  • miRNA target prediction
  • Appendices. Usage of internet for bioinformatics
  • important web resources for bioinformatics databases and tools
  • NCBI database: a brief account
  • EMBL databases and tools: an overview
  • Basics of molecular phylogeny
  • Evolutionary models of molecular phylogeny.

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