Genomic Perl : from bioinformatics basics to working code / Rex A. Dwyer.

Format:

Book

Author/Creator:

Dwyer, Rex A., author.

Language:

English

Subjects (All):

Perl (Computer program language).

Molecular biology--Data processing.

Molecular biology.

Bioinformatics.

Physical Description:

1 online resource (xvii, 334 pages) : digital, PDF file(s).

Edition:

1st ed.

Place of Publication:

Cambridge : Cambridge University Press, 2003.

Language Note:

English

Summary:

This introduction to computational molecular biology will help programmers and biologists learn the skills needed to start work in this important, expanding field. The author explains many of the basic computational problems and gives concise, working programs to solve them in the Perl programming language. With minimal prerequisites, the author explains the biological background for each problem, develops a model for the solution, then introduces the Perl concepts needed to implement the solution. The book covers pairwise and multiple sequence alignment, fast database searches for homologous sequences, protein motif identification, genome rearrangement, physical mapping, phylogeny reconstruction, satellite identification, sequence assembly, gene finding, and RNA secondary structure. The concrete examples and step-by-step approach make it easy to grasp the computational and statistical methods, including dynamic programming, branch-and-bound optimization, greedy methods, maximum likelihood methods, substitution matrices, BLAST searching, and Karlin-Altschul statistics. Perl code is provided on the accompanying CD.

Contents:

Cover; Half-title; Title; Copyright; Dedication; Contents; Preface; Acknowledgments; CHAPTER ONE The Central Dogma; CHAPTER TWO RNA Secondary Structure; CHAPTER THREE Comparing DNA Sequences; CHAPTER FOUR Predicting Species: Statistical Models; CHAPTER FIVE Substitution Matrices for Amino Acids; CHAPTER SIX Sequence Databases; CHAPTER SEVEN Local Alignment and the BLAST Heuristic; CHAPTER EIGHT Statistics of BLAST Database Searches; CHAPTER NINE Multiple Sequence Alignment I; CHAPTER TEN Multiple Sequence Alignment II; CHAPTER ELEVEN Phylogeny Reconstruction

CHAPTER TWELVE Protein Motifs and PROSITECHAPTER THIRTEEN Fragment Assembly; CHAPTER FOURTEEN Coding Sequence Prediction with Dicodons; CHAPTER FIFTEEN Satellite Identification; CHAPTER SIXTEEN Restriction Mapping; CHAPTER SEVENTEEN Rearranging Genomes: Gates and Hurdles; APPENDIX A Drawing RNA Cloverleaves; APPENDIX B Space-Saving Strategies for Alignment; APPENDIX C A Data Structure for Disjoint Sets; APPENDIX D Suggestions for Further Reading; Bibliography; Index

Notes:

Title from publisher's bibliographic system (viewed on 05 Oct 2015).

Includes bibliographical references (p. 318-323) and index.

ISBN:

1-107-13046-8

1-280-41821-4

9786610418213

1-139-16476-7

1-139-14710-2

0-511-18056-X

0-511-05706-7

0-511-30755-1

0-511-07185-X

OCLC:

437068906