Description
SPRINGER Bioinformatics For Evolutionary Biologists 1St Edition by Bernhard Haubold
This self-contained textbook covers fundamental aspects of sequence analysis in evolutionary biology, including sequence alignment, phylogeny reconstruction, and coalescent simulation. It addresses these aspects through a series of over 400 computer problems, ranging from elementary to research level to enable learning by doing. Students solve the problems in the same computational environment used for decades in science - the UNIX command line. This is available on all three major operating systems for PCs: Microsoft Windows, Mac-OSX, and Linux. To learn using this powerful system, students analyze sample sequence data by applying generic tools, bioinformatics software, and over 40 programs specifically written for this course. The solutions for all problems are included, making the book ideal for self-study. Problems are grouped into sections headed by an introduction and a list of new concepts and programs. By using practical computing to explore evolutionary concepts and sequence data, the book enables readers to tackle their own computational problems. Part I UNIX.- 1 Getting Started.- 2 Files.- 3 Scripts. Part II Optimal Alignment.- 4 Sequence Evolution.-and Alignment.- 5 Amino Acid Substitution Matrices.- 6 Protein Evolution.- 7 The Number of Possible Alignments.- 8 Dot Plots.- 9 From Dot Plot to Alignment.- 10 Optimal Global Alignment.- 11 Age of the Adh/Adh-dup Gene Duplication in Drosophila.- 12 Optimal and Simplified Local Alignment.- Part III Exact Matching.- Classical Methods.- 14 Suffix Trees.- 16 Text Compression.- Part IV Fast Alignment.-17 Shotgun Sequencing.- 18 Fast Global Alignment.- 19 Fast Local Alignment.- 20 Statistics of Local Alignments.- 21 Clustering of the M. genitalium Proteome.- 22 Position-Dependent Amino Acid Score Matrix: PSI-BLAST.- 23 Optimal Multiple Sequence Alignment.- 24 Heuristic Multiple Sequence Alignment.- Part V Phylogeny.- 26 Rooted Phylogeny.- 27 Unrooted Phylogeny.- Part VI Coalescent.-28 Ancestors.- 29 The Wright-Fisher Model.- 30 The Coalescent.- 31 The Coalescent with Recombination.- Part VII Answers.- References