Summary: Fundamental Concepts of Bioinformatics is the first textbook co-authored by a biologist and computer scientist that is specifically designed to make bioinformatics accessible to undergraduates and prepare them for more advanced work. Students learn what programs are available for analyzing data, how to understand the basic algorithms that underlie these programs, what bioinformatic research is like, and other basic concepts. Information flows easily from one topic to
the next, with enough detail to support the major concepts without overwhelming students. Problems at the end of each chapter use real data to help students apply what they have learned so they know how to critically evaluate results from both a statistical and biological point of view.
Summary: Fundamental Concepts of Bioinformatics is the first textbook co-authored by a biologist and computer scientist that is specifically designed to make bioinformatics accessible to undergraduates and prepare them for more advanced work. Students learn what programs are available for analyzing data, how to understand the basic algorithms that underlie these programs, what bioinformatic research is like, and other basic concepts. Information flows easily from one topic to the next, with enough detail to support the major concepts without overwhelming students. Problems at the end of each chapter use real data to help students apply what they have learned so they know how to critically evaluate results from both a statistical and biological point of view. ...show less
Edition/Copyright:03 Cover: Paperback Publisher:Benjamin-Cummings Publishing Co. Published: 09/12/2002 International: No
View Table of Contents
I. MOLECULAR BIOLOGY AND BIOLOGICAL CHEMISTRY.
The genetic material.
Nucleotides. Orientation. Base pairing. The central dogma of molecular biology.
Gene structure and information content.
Promoter sequences. The genetic code. Open reading frames. Introns and exons.
Protein structure and function.
Primary structure. Secondary, tertiary and quaternary structure.
The nature of chemical bonds.
Anatomy of an atom. Valence. Electronegativity. Hydrophilicity and hydrophobicity.
Molecular biology tools.
Restriction enzymes. Gel electrophoresis. Blotting, hybridization and microarrays. Cloning. Polymerase chain reaction (PCR). DNA sequencing.
Genomic information content.
C value paradox. Reassociation kinetics.
II. DATA SEARCHES AND PAIRWISE ALIGNMENTS.
Dot plots. Simple alignments. Scoring. Gaps.
Simple gap penalties. Origination and length penalties.
Scoring matrices. Dynamic programming: The Needleman and Wunsch algorithm. Local and global alignments.
Global and Semi-global alignments. The Smith-Waterman algorithm.
BLAST and its relatives. Other algorithms.
Multiple sequence alignments.
III. SUBSTITUTION PATTERNS.
Patterns of substitutions within genes.
Mutation rates. Functional constraint. Synonymous vs. nonsynonymous changes. Indels and psuedogenes. Substitutions vs. mutations. Fixation.
Estimating substitution numbers.
Jukes/Cantor model. Transitions and transversions. Kimura's two-parameter model. Models with even more parameters. Substitutions between protein sequences.
Variations in substitution rates between genes. Molecular clocks.
Relative rate tests. Causes of rate variation in lineages.
Evolution in organelles.
IV. DISTANCE-BASED METHODS OF PHYLOGENETICS.
History of molecular phylogenetics. Advantages to molecular phylogenies. Phylogenetic trees.
Terminology of tree reconstruction. Rooted and unrooted trees. Gene vs. species trees. Character and distance data.
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