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Contents (Xia, X. 2007. Bioinformatics and the cell. Springer)

  • Preface
  • Acknowledgement
  • Chapter 1 BLAST and FASTA
    1. Introduction
    2. Mathematics of string matching
    3. String-matching algorithms in FASTA and
    4. Homology search and sequence annotation
    5. Postscript
  • Chapter 2 Sequence alignment
    1. Introduction
    2. Pairwise alignment
    3. Multiple sequence alignment
    4. Sequence alignment with secondary structure
    5. Align nucleotide sequences against amino acid sequences
    6. Postscript
  • Chapter 3 Contig assembly
    1. Introduction
    2. Skeletal output of contig assembly
    3. string matching of two sequence ends
    4. New development in contig assembly
    5. Postscript
  • Chapter 4 DNA replication and viral evolution
    1. Introduction
    2. Fundamentals of viruses
    3. Fundamentals of bacterial species
    4. Genomic AT% of bacterial species is indicative of cellular AT availability
    5. Formulating the hypothesis and predictions
    6. Are our predictions supported?
    7. A short play featuring phages and bacteria
  • Chapter 5 Gene and motif prediction
    1. Introduction
    2. Bayes’ theorem and odds ratios
    3. Characterizing features of Signal sensor
      1. Position weight matrix
      2. Perceptron
    4. Characterizing features of Content sensors
  • Chapter 6 Hidden Markov Models
    1. Introduction
    2. Markov models
    3. Hidden Markov Models
      1. The Essential Elements in a Hidden Markov Model
      2. Training HMM
      3. The Viterbi algorithm
      4. Forward algorithm
      5. HMM and gene prediction
    4. Postscript
  • Chapter 7 Gibbs Sampler
    1. Introduction
    2. A numerical illustration of the computational details of Gibbs sampler
      1. Initialization
      2. Predictive update
    3. Motif sampler
  • Chapter 8. Bioinformatics and vertebrate mitochondria
    1. Introduction
      1. Mitochondria and mitochondrial genomes
      2. DNA-Replication and Strand-biased mutation spectrum
      3. The effect of strand-biased mutation on codon usage
    2. Three hypotheses on tRNA anticodon
      1. The mutation hypothesis
      2. The codon-anticodon adaptation hypothesis
      3. The wobble versatility hypothesis
    3. Empirical evaluation of the three alternative hypotheses
    4. Integrating the codon-anticodon adaptation hypothesis (CAAH) and the wobble versatility hypothesis (WVH)
    5. Conflict between translation initiation and elongation
    6. Postscript
  • Chapter 9. Characterizing translation efficiency
    1. Introduction
    2. RSCU (Relative synonymous codon usage
    3. CAI (Codon adaptation index)
    4. Indices of codon-anticodon adaptation
    5. Why CAI or CAAI should not be taken as a measure of gene expression?
    6. Will AT-rich mRNA be translated inefficiently?
    7. Codon adaptation index and proteomics: clarification of some misunderstandings
  • Chapter 10 Protein isoelectric point
    1. Introduction
    2. Amino acid and protein isoelectric point
    3. Genomic profiling of protein isoelectric point: a case study with Helicobacter pylori
    4. An alternative explanation of H. pylori data
  • Chapter 11 Bioinformatics and Two-Dimensional Protein Separation
    1. Introduction
    2. Scientific rationale behind the 2D-SDS-PAGE
    3. Expected separation pattern of 2D-SDS-PAGE for the genome-derived proteome
    4. Posttranslational modification
  • Chapter 12 Self-Organizing Map and other clustering Algorithms
    1. Introduction
      1. Classification and clustering
      2. Clustering and gene expression
      3. Similarity and distance indices
    2. UPGMA
    3. Self-organizing map (SOM)
      1. The SOM algorithm
      2. Variations of the basic SOM algorithm
  • Chapter 13 Molecular Phylogenetics
    1. Introduction
    2. Biodiversity, historical information, and phylogenetics
    3. Substitution models
    4. Tree-building methods
      1. Distance-based methods
      2. Maximum parsimony methods
      3. Maximum likelihood methods
      4. Bayesian inference
  • Chapter 14 Fundamentals of Proteomics
    1. Introduction
    2. Protein Mass Spectrometry
    3. Charge deconvolution
    4. Peptide mass fingerprinting

From: Xia, X. 2007. Bioinformatics and the cell: modern computational approaches in genomics, proteomics and transcriptomics. Springer URL link. 361 pp.

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