List of Tables
1 Chapter 1Table 1.1 Indicating locations within the feature table.
2 Chapter 2Table 2.1 Entrez Boolean search statements.
3 Chapter 3Table 3.1 Selecting an appropriate scoring matrix.Table 3.2 BLAST algorithms.Table 3.3 Main FASTA algorithms.
4 Chapter 7Table 7.1 Disorder prediction performance.Table 7.2 Performance of selected gene ontology term prediction methods in CAFA2...
5 Chapter 8Table 8.1 Aligner performance on BAliBASE3 benchmark.
6 Chapter 9Table 9.1 Some common software packages implementing different phylogenetic anal...
7 Chapter 11Table 11.1 List of common sources of protein sequences (used in FASTA format).Table 11.2 Standard search parameters used with sequence database search engines...
8 Chapter 12Table 12.1 Relationship between backbone root mean square deviation (RMSD, i...
9 Chapter 14Table 14.1 A list of freely available molecular editors and visualization tools.Table 14.2 A list of open access chemical, spectral, pathway, and metabolomic da...
10 Chapter 15Table 15.1 Examples of genes that have undergone natural selection in human popu...
11 Chapter 17Table 17.1 Examples of commonly used biomedical ontologies and terminologies in ...
12 Chapter 18Table 18.1 Common parametric statistical tests and their non-parametric equivale...
List of Illustrations
1 Chapter 1Figure 1.1 The landing page for ENA record U54469.1, providing a graphical vie...Figure 1.2 Results of a search for the human heterogeneous nuclear ribosomal p...Figure 1.3 The Subcellular location and Pathology & Biotech sections of ...Figure 1.4 The Feature viewer rendering of the record for the human heterogene...Figure 1.5 Expanding the PTM, Structural features, and Variants sections withi...
2 Chapter 2Figure 2.1 The exponential growth of GenBank in terms of number of nucleotides...Figure 2.2 Results of a text-based Entrez query against PubMed using Boolean o...Figure 2.3 An example of a PubMed record in Abstract format, as returned throu...Figure 2.4 Neighbors to an entry found in PubMed. The original entry from Figu...Figure 2.5 The Entrez Gene page for the DCC (deleted in colorectal carcinoma) ...Figure 2.6 A section of the Database of Single Nucleotide Polymorphisms (dbSNP...Figure 2.7 Entries in the RefSeq protein database corresponding to the origina...Figure 2.8 The RefSeq entry for the netrin receptor, the protein product of th...Figure 2.9 The same RefSeq entry for the netrin receptor shown in Figure 2.8, ...Figure 2.10 Protein structures associated with the RefSeq entry for the human ...Figure 2.11 The structure summary page for pdb:4URT, the crystal structure of ...Figure 2.12 A list of structures deemed similar to pdb:4URT using VAST+. The t...Figure 2.13 Online Mendelian Inheritance in Man (OMIM) entries related to the Figure 2.14 The Online Mendelian Inheritance in Man (OMIM) entry for the DCC g...Figure 2.15 An example of a list of allelic variants that can be found through...Figure 2.16 The ClinicalTrials.gov page showing all actively recruiting clinic...Figure 2.17 A clickable map showing where actively recruiting clinical trials ...Figure 2.18 The Mouse Genome Informatics (MGI) entry for the Dcc gene in mouse...Figure 2.19 The Zebrafish Information Network (ZFIN) gene page for the dcc gen...Figure 2.20 An example of gene expression data available through the Zebrafish...
3 Chapter 3Figure 3.1 The BLOSUM62 scoring matrix (Henikoff and Henikoff 1992). BLOSUM62 ...Figure 3.2 A nucleotide scoring table. The scoring for the four nucleotide bas...Figure 3.3 The initiation of a BLAST search. The search begins with query word...Figure 3.4 BLAST search extension. Length of extension represents the number o...Figure 3.5 The National Center for Biotechnology Information (NCBI) BLAST land...Figure 3.6 The upper portion of the BLASTP query page. The first section in th...Figure 3.7 The lower portion of the BLASTP query page, showing algorithm param...Figure 3.8 Graphical display of BLASTP results. The query sequence is represen...Figure 3.9 The BLASTP “hit list.” For each sequence found, the user is present...Figure 3.10 Detailed information on a representative BLASTP hit. The header pr...Figure 3.11 Performing a BLAST 2 Sequences alignment. Clicking the check box a...Figure 3.12 Typical output from a BLAST 2 Sequences alignment, based on the qu...Figure 3.13 Constructing a position-specific scoring matrix (PSSM). In the upp...Figure 3.14 Performing a PSI-BLAST search. See text for details.Figure 3.15 Selecting algorithm parameters for a PSI-BLAST search. See text fo...Figure 3.16 Results of the first round of a PSI-BLAST search. For each sequenc...Figure 3.17 Results of the second round of a PSI-BLAST search. New sequences i...Figure 3.18 Submitting a BLAT query. A rat clone from the Cancer Genome Anatom...