Genomic Perl

From Bioinformatics Basics to Working Code

Rex A. Dwyer

350 pages, parution le 11/02/2003

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Résumé

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

The Central Dogma
RNA Secondary Structure
Comparing DNA Sequences
Predicting Species: Statistical Models
Substitution Matrices for Amino Acids
Sequence Databases
Local Alignment and the BLAST Heuristic
Statistics of BLAST Database Searches
Multiple Sequence Alignment I
Multiple Sequence Alignment II
Phylogeny Reconstruction
Protein Motifs and PROSITE
Fragment Assembly
Coding Sequence Prediction with Dicodons
Satellite Identification
Restriction Mapping
Rearranging Genomes: Gates and Hurdles

A. Drawing RNA Cloverleaves
B. Space-Saving Strategies for Alignment
C. A Data Structure for Disjoint Sets
D. Suggestions for Further Reading

Caractéristiques techniques

	PAPIER
Éditeur(s)	Cambridge University Press
Auteur(s)	Rex A. Dwyer
Parution	11/02/2003
Nb. de pages	350
Format	18 x 26
Couverture	Relié
Poids	801g
Intérieur	Noir et Blanc
EAN13	9780521801775
ISBN13	978-0-521-80177-5