• Home
  • Chapter 1: Bioinformatics and Genomic Data: Investigating a Complex Genetic Disease
  • Chapter 2: Computational Manipulation of DNA: Genetic Screening for Disease Alleles
  • Chapter 3: Sequence Alignment: Investigating an Influenza Outbreak
  • Chapter 4: Database Searching and Multiple Alignment: Investigating Antibiotic Resistance
  • Chapter 5: Substitution Matrices and Protein Alignments: Virulence Factors in E. coli
  • Chapter 6: Distance Measurement in Molecular Phylogenetics: Evolution of Mammals
  • Chapter 7: Tree Building in Molecular Phylogenetics: The Three Domains of Life
  • Chapter 8: DNA Sequencing: Identification of Novel Viral Pathogens
  • Chapter 9: Sequence-Based Gene Prediction: Annotation of a Resistance Plasmid
  • Chapter 10: Advanced Gene Prediction: Identification of an Influenza Resistance Gene
  • Chapter 11: Protein Structure Prediction and Analysis: Rational Drug Design
  • Chapter 12: Nucleic Acid Structure Prediction: PCR and RNAi
  • Downloadable Files

Welcome to the Companion Website dedicated to the text Exploring Bioinformatics, Second Edition.

This Website is designed to:

  • Provide you with study aids to prepare for your class
  • Help you master the material in the text
  • Expand the scope of the textbook
  • Grant you access to up-to-date information

Student Resources

Chapter 1: Bioinformatics and Genomic Data: Investigating a Complex Genetic Disease
The goal of this chapter is to build skills in retrieving information from genomic databases. Click here for all chapter resources.

Chapter 2: Computational Manipulation of DNA: Genetic Screening for Disease Alleles
The primary goal of this chapter is to give students in programming-oriented courses experience with manipulating strings in the language by writing relatively short and straightforward programs. Click here for all chapter resources.

Chapter 3: Sequence Alignment: Investigating an Influenza Outbreak
This chapter focuses on algorithms for optimal alignment of DNA sequences. Click here for all chapter resources.

Chapter 4: Database Searching and Multiple Alignment: Investigating Antibiotic Resistance
This chapter develops skills in two very commonly used types of Web-based bioinformatics tools: BLAST and ClustalW. Click here for all chapter resources.

Chapter 5: Substitution Matrices and Protein Alignments: Virulence Factors in E. coli
This chapter extends our understanding of alignment to the amino-acid sequences of proteins, introducing the idea of scoring matrices based on amino-acid similarity. Click here for all chapter resources.

Chapter 6: Distance Measurement in Molecular Phylogenetics: Evolution of Mammals
Methods of reconstructing evolutionary history are the focus of this chapter, more specifically dealing with measurement of evolutionary distance. Click here for all chapter resources.

Chapter 7: Tree Building in Molecular Phylogenetics: The Three Domains of Life
This chapter deals with the key problem of tree-building: how to use computational methods to obtain biologically relevant groupings of species in a phylogenetic tree. Click here for all chapter resources.

Chapter 8: DNA Sequencing: Identification of Novel Viral Pathogens
This chapter focuses on how bioinformatics is essential for assembly of short sequences into complete gene or genome sequences and for applications that use the short sequences themselves. Click here for all chapter resources.

Chapter 9: Sequence-Based Gene Prediction: Annotation of a Resistance Plasmid
In this chapter, sequence-based methods suitable for gene prediction in prokaryotes are explored and their value and limitations in eukaryotic gene discovery examined. Click here for all chapter resources.

Chapter 10: Advanced Gene Prediction: Identification of an Influenza Resistance Gene
This chapter builds on the sequence-based gene prediction methods discussed in Chapter 9 and examines content-based and probabilistic methods of gene discovery. Click here for all chapter resources.

Chapter 11: Protein Structure Prediction and Analysis: Rational Drug Design
In this chapter, you’ll use Web-based software to model protein structure and see how such molecular modeling can aid in drug design. Click here for all chapter resources.

Chapter 12: Nucleic Acid Structure Prediction: PCR and RNAi
This chapter focuses on the structure of nucleic acids. Click here for all chapter resources.