Bioinformatics

8 Chapter 8Figure 8.1 An example multiple sequence alignment of seven globin protein sequ...Figure 8.2 An outline of the simple progressive multiple alignment process. Th...Figure 8.3 Aligner accuracy versus total single-threaded run time using the BA...Figure 8.4 Total single-threaded execution time ( y -axis) for different aligner...Figure 8.5 Ratio of total run time relative to single-threaded execution ( y -ax...Figure 8.6 Protein and RNA multiple sequence alignments as visualized using Ja...Figure 8.7 Linked coding sequence (CDS), protein, and three-dimensional struct...

9 Chapter 9Figure 9.1 Different ways to visualize a tree. In this example, the same tree ...Figure 9.2 Alignments illustrating sequence similarity versus sequence identit...Figure 9.3 The differences between orthologs, paralogs, and xenologs. The ance...Figure 9.4 The difference between phylogenetic signal and phylogenetic noise. ...Figure 9.5 Character-based versus distance-based phylogenetic methods. Charact...Figure 9.6 Rooting a tree with an outgroup. Escherichia coli bacteria are comm...Figure 9.7 Workflow for a protein-based phylogenetic analysis using the PHYLIP...Figure 9.8 Phylogenetic relationships can be visualized using different types ...Figure 9.9 Excerpt of a Salmonella minimum spanning tree. Types of Salmonella ...

10 Chapter 10Figure 10.1 Example of an MA plot before (a) and after (b) normalization. A , o...Figure 10.2 Histogram of the base mismatch (MM) rate across multiple RNA-seq s...Figure 10.3 Overview of quantile normalization. We start with the box on the t...Figure 10.4 Batch effects principal components analysis (PCA) example. Boxplot...Figure 10.5 A simple illustration of the process of hierarchical clustering. (...Figure 10.6 Heatmap showing clustering of gene expression data of the 100 most...Figure 10.7 First two components of principal component analysis (PCA) on the ...Figure 10.8 Principal component analysis (PCA) is a dimensionality reduction m...Figure 10.9 Illustration of how one can select k when performing consensus clu...Figure 10.10 Receiver operating characteristic (ROC) curve for a model desig...

11 Chapter 11Figure 11.1 Gene(s) to proteoforms. This figure illustrates the complexity of ...Figure 11.2 Quadrupole mass analyzer. Schematic of a quadrupole mass analyzer,...Figure 11.3 Time of flight (TOF) mass analyzer. Schematic of a TOF mass analyz...Figure 11.4 (a) Tandem mass spectrometry (MS). Schematic of a triple quadrupol...Figure 11.5 Fragmentation tandem mass spectrometry (MS/MS, or MS 2) spectrum. A...Figure 11.6 Polypeptide backbone cleavage produces different product ion speci...Figure 11.7 Post-translational modifications (PTMs) take place at different am...Figure 11.8 Data pre-processing workflow of a mass spectrum. Different steps i...Figure 11.9 Shotgun proteomics workflow. Schematic showing different steps inv...Figure 11.10 A schematic diagram comparing the label-free approach with the di...Figure 11.11 Peptide mass fingerprinting (PMF) workflow. Schematic showing dif...Figure 11.12 Mascot peptide mass fingerprinting (PMF). PMF submission screen a...Figure 11.13 Peptide sequencing via tandem mass spectrometry (MS/MS) spectra i...Figure 11.14 Peptide sequence tag searching. Schematic illustrating how a sequ...Figure 11.15 Peptide spectrum match (PSM). Annotated MS 2spectrum showing matc...Figure 11.16 Mascot search engine. Mascot MS 2database search submission windo...Figure 11.17 Proteomics. A broad classification of proteomics and the biologic...

12 Chapter 12Figure 12.1 A flow diagram illustrating the steps used to experimentally prepa...Figure 12.2 An example of a nuclear magnetic resonance (NMR) “blurrogram” of a...Figure 12.3 The different levels of protein structures illustrating: (a) prima...Figure 12.4 Examples of different types of protein folds including (a) the fou...Figure 12.5 An illustration of standard amino acid residue and peptide bond ge...Figure 12.6 An example of a Protein Data Bank formatted file showing the first...Figure 12.7 A Ramachandran plot for the thioredoxin protein (Protein Data Bank...Figure 12.8 A screenshot of the Research Collaboratory for Structural Bioinfor...Figure 12.9 A screenshot of an image of Escherichia coli thioredoxin as genera...Figure 12.10 An illustration of the four major approaches to rendering protein...Figure 12.11 An example of the high-quality images that can be created using a...Figure 12.12 An illustration of a homology model (b) of Escherichia coli thior...Figure 12.13 A schematic illustration of how threading is performed. (a) A que...Figure 12.14 An example of the high-quality postscript output data from PROCHE...Figure 12.15 An example of the CATH database description of Escherichia coli t...

13 Chapter 13Figure 13.1 The Reactome database pathway view. The central view shows pathway...Figure 13.2 The EcoCyc database cellular overview of Escherichia coli metaboli...Figure 13.3 An example of metabolic pathway reconstruction from Kyoto Encyclop...Figure 13.4 A BioGRID database record. A screenshot of the result page for a B...Figure 13.5 An IntAct database search for the human MDM2 gene. A summary of al...Figure 13.6 An example of the main STRING query result page. A network of rela...Figure 13.7 A query result from GeneMANIA. Each node in the network represents...Figure 13.8 The AKT pathway as represented by a traditional method (top left, ...Figure 13.9 The main components of the Proteomics Standards Initiative–Molecul...Figure 13.10 The valine biosynthesis pathway dynamically drawn by the Pathway ...Figure 13.11 Output from the PathVisio software showing a portion of a human c...Figure 13.12 The set of symbol types available in the Systems Biology Graphica...Figure 13.13 The Drosophila melanogaster cell cycle drawn using Systems Biolog...Figure 13.14 The results of pathway enrichment analysis using the g:Profiler t...Figure 13.15 A Gene Set Enrichment Analysis (GSEA) enrichment figure. The bott...Figure 13.16 An enrichment map showing two enriched themes. Each node represen...Figure 13.17 An introduction to terminology and visual notation used in the co...Figure 13.18 Zooming in on a network in Cytoscape shows part of a large connec...Figure 13.19 An overview of a pathway analysis workflow, summarizing multiple ...

14 Chapter 14Figure 14.1 A diagram illustrating the typical workflow for a metabolomic expe...Figure 14.2 An example of a Molecular Design Limited (MDL) chemical fingerprin...Figure 14.3 An example of a MOL file for a two-dimensional representation of L...Figure 14.4 An example of an nmrML data file for L-alanine. The actual file is...Figure 14.5 The JSpectraViewer image for L-alanine. JSpectraViewer is a Java a...Figure 14.6 A selection of two screenshots from the PubChem web pages for the ...Figure 14.7 Two screenshots of the gas chromatography–mass spectrometry (GC-MS...Figure 14.8 Two screenshots from the Human Metabolome Database (HMDB) entry fo...Figure 14.9 A simplified illustration of how spectral deconvolution works for ...Figure 14.10 Two screenshots of the Bayesil web server. (a) A nuclear magnetic...Figure 14.11 An illustration of how spectral deconvolution works for gas chrom...Figure 14.12 An illustration of how principal component analysis can be though...Figure 14.13 A three-dimensional principal component analysis (PCA) “scores” p...Figure 14.14 The MetaboAnalyst Module Overview page. This page allows users to...Figure 14.15 The MetaboAnalyst Data Upload page. This page allows users to upl...Figure 14.16 The MetaboAnalyst Data Normalization page. The optimal normalizat...Figure 14.17 The MetaboAnalyst Data Normalization and Scaling results, generat...Figure 14.18 A two-dimensional principal component analysis (PCA) “scores” plo...Figure 14.19 The principal component analysis (PCA) “loadings” plot, showing t...Figure 14.20 The partial least squares discriminant analysis (PLS-DA) plot sho...Figure 14.21 An example of an R 2/ Q 2plot generated by MetaboAnalyst using the ...Figure 14.22 A variable importance in projection plot showing which metabolite...Figure 14.23 A pathway impact plot showing the importance of different pathway...