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Bioinformatics: A Biologist's Guide to Biocomputing and the Internet

Table of Contents

Section I: An Overview of Bioinformatics

1. Introduction A Bioinformatics Survival Guide, Integration of Software, Databases, and the Web

2. Genomics and the Genome Project Genomics, Genome Sequencing, Raw Genome Sequence Data, Expressed Sequence Tags, Polymorphisms, Genome Bioinformatics, The Genome Project and the Internet, Genomics and Pharmaceutical Research

3. The Role of Computers in the Biology Laboratory Computers in the Lab, A Brief History of the Internet, Using Computers for Biology Research, Types of Computers, Network Computers, Working with Mainframes, Personal Computers, and the Web, Why GCG?

Section II: Computer Tools for Sequence Analysis

4. Finding and Retrieving Sequence in Databases Public Databases, Entrez, SRS, GCG LOOKUP and FETCH programs

5. Similarity Searching Introduction to Sequence Similarity, Dot Plots, Distances, Similarity Searches on the WWW, Databases, FASTA, FASTA Format, BLAST, BLAST Considerations, BLAST vs. FASTA, General Tips for Similarity Searching, Other Similarity Search Methods, Interpretation of Output

6. Pairwise and Multiple Alignment Introduction to Alignment, Global vs. Local Alignments, Multiple Sequence Alignment, Editing and Formatting Multiple Alignments

7. Structure-Function Relationships Finding Genes in DNA Sequences, DNA Signal Sequences, RNA Structure, Protein Composition and Secondary Structure, Protein Tertiary Structure, Motifs, Profiles, Searching for New Motifs

8. Plasmid Mapping and PCR Primer Design Restriction Mapping, DNA Strider, MacVector OMIGA, Gene Construction Kit, Vector NTI, Primer Design for PCR & Sequencing, Primer Design Programs

9. DNA Sequencing The Biochemistry of DNA Sequencing, Sequencing Strategies, Software Recommendations

10. Phylogenetics Taxonomy and Phylogenetics, Some Caveats, Cladistic vs. Phenetic Analysis Methods, Calculating Distances, Clustering Algorithms, Cladistic Methods: Parsimony, Cladistic Methods: Maximum Likelihood, Computer Software

Appendices

I. A list of useful websites and software archives

II. Software on the CD-ROM (for both Mac & Windows) Free (or shareware) DNA Strider 1.1 PHYLIP MacClade CN3D RasMol CHIME FoldIt GCGFigure ABI EditView MacBoxshade MacPattern ANTHEPROT ClustalX MACAW SeqVu Se-Al Oligo MacVector OMIGA RightPrimer Plasmid Artist Sequencher Vector NTI Gene Construction Kit Gene Inspector GeneTool/PepTool

Demo Versions of Commercial Products

Technical Difficulties? Please e-mail