4 Chapter 4Figure 4.1 The home page of the UCSC Genome Browser, showing a query for the g...Figure 4.2 The default view of the UCSC Genome Browser, showing the genomic co...Figure 4.3 The genomic context of the human HIF1A gene, after clicking on zoom...Figure 4.4 The RefSeq Track Settings page. The track settings pages are used t...Figure 4.5 The genomic context of the human HIF1A gene, after displaying RefSe...Figure 4.6 The Get Genomic Sequence page that provides an interface for users ...Figure 4.7 The genomic context of the human HIF1A gene, after changing the dis...Figure 4.8 Configuring the track settings for the Common SNPs(150) track. Set ...Figure 4.9 The genomic context of the human HIF1A gene, after changing the col...Figure 4.10 The GTEx Gene track, which depicts median gene expression levels i...Figure 4.11 BLAT search at the UCSC Genome Browser. (a) This page shows the re...Figure 4.12 Configuring the UCSC Table Browser. The link to the Table Browser ...Figure 4.13 The home page of the Ensembl Genome Browser, showing a query for t...Figure 4.14 The Gene tab for the human PAH gene. This landing page provides li...Figure 4.15 Computationally predicted orthologs of the human PAH gene, from th...Figure 4.16 The Location tab for the human PAH gene. The Location tab is divid...Figure 4.17 Zooming in on the bottom section of the Location tab from Figure 4...Figure 4.18 The Ensembl Variant tab. (a) To get more details about SNP rs76296...Figure 4.19 The Ensembl Regulatory Build track. (a) Go to Configure this page ...Figure 4.20 The Synteny view at Ensembl. (a) An overview of the syntenic block...Figure 4.21 Ensembl BLAST output, showing an alignment between the human ADAM1...Figure 4.22 Using BioMart to retrieve the mouse orthologs of the human RefSeqs...Figure 4.23 JBrowse display of a predicted Mnemiopsis gene (ML05372a) from the...
5 Chapter 5Figure 5.1 A simplified depiction of a prokaryotic gene or open reading frame ...Figure 5.2 A simplified depiction of a eukaryotic gene illustrating the multi-...Figure 5.3 A schematic illustration of the upstream regions of a eukaryotic ge...Figure 5.4 A schematic illustration of the splice site regions around exons an...Figure 5.5 Sample output from a GENSCAN analysis of the uroporphyrinogen decar...Figure 5.6 Schematic representation of measures of gene prediction accuracy at...Figure 5.7 The typical L-shaped structure of a tRNA molecule. This depicts the...Figure 5.8 A screenshot montage of the PHASTER web server showing the website ...Figure 5.9 A screenshot of a BASys bacterial genome annotation output for the ...
6 Chapter 6Figure 6.1 The three levels of organization of RNA structure. (a) The primary ...Figure 6.2 The RNA secondary structure of the 3′ untranslated region of the Dr...Figure 6.3 An illustration of the equilibria of RNA structures in solution. (a...Figure 6.4 Prediction of conformational free energy for a conformation of RNA ...Figure 6.5 A simple RNA pseudoknot. This figure illustrates two representation...Figure 6.6 The input form for the version 3.1 Mfold server. (a) The top and (b...Figure 6.7 The output page for the Mfold server. Please refer to the text for ...Figure 6.8 Sample output from the Mfold web server, version 3.1. (a) The secon...Figure 6.9 RNAstructure web server input form. (a) The top and (b) the bottom ...Figure 6.10 Sample output from the RNAstructure web server showing the predict...Figure 6.11 Input form for the RNAstructure web server for multiple-sequence p...Figure 6.12 Sample output from the RNAstructure web server for multiple-sequen...
7 Chapter 7Figure 7.1 Dashboard of the PredictProtein web server. PredictProtein (Yachdav...Figure 7.2 Protein secondary structure. Experimentally determined three-dimens...Figure 7.3 Accessible surface area (ASA). The ASA describes the surface that i...Figure 7.4 Protein secondary structure. Prediction of secondary structure, sol...Figure 7.5 Types of transmembrane proteins. Experimentally determined three-di...Figure 7.6 Transmembrane helix prediction by TMSEG. TMSEG (Bernhofer et al. 20...Figure 7.7 Annotations of human tumor suppressor P53 (P53_HUMAN). (a) InterPro...Figure 7.8 Prediction of subcellular localization. Visual output from LocTree3...Figure 7.9 From predicting single amino acid sequence variant (SAV) effects to...
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