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.