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Genomic Perl

Author: Rex A. Dwyer
Publisher: Cambridge University Press
ISBN: 9780521801775
Size: 74.25 MB
Format: PDF, ePub, Mobi
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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.

Combinatorial Pattern Matching Algorithms In Computational Biology Using Perl And R

Author: Gabriel Valiente
Publisher: CRC Press
ISBN: 9781420069747
Size: 17.31 MB
Format: PDF, Mobi
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Emphasizing the search for patterns within and between biological sequences, trees, and graphs, Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R shows how combinatorial pattern matching algorithms can solve computational biology problems that arise in the analysis of genomic, transcriptomic, proteomic, metabolomic, and interactomic data. It implements the algorithms in Perl and R, two widely used scripting languages in computational biology. The book provides a well-rounded explanation of traditional issues as well as an up-to-date account of more recent developments, such as graph similarity and search. It is organized around the specific algorithmic problems that arise when dealing with structures that are commonly found in computational biology, including biological sequences, trees, and graphs. For each of these structures, the author makes a clear distinction between problems that arise in the analysis of one structure and in the comparative analysis of two or more structures. He also presents phylogenetic trees and networks as examples of trees and graphs in computational biology. This book supplies a comprehensive view of the whole field of combinatorial pattern matching from a computational biology perspective. Along with thorough discussions of each biological problem, it includes detailed algorithmic solutions in pseudo-code, full Perl and R implementation, and pointers to other software, such as those on CPAN and CRAN.

Annual Review Of Information Science And Technology

Author: Blaise Cronin
Publisher: Information Today, Inc.
ISBN: 9781573872096
Size: 76.41 MB
Format: PDF, ePub, Mobi
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ARIST, published annually since 1966, is a landmark publication within the information science community. It surveys the landscape of information science and technology, providing an analytical, authoritative, and accessible overview of recent trends and significant developments. The range of topics varies considerably, reflecting the dynamism of the discipline and the diversity of theoretical and applied perspectives. While ARIST continues to cover key topics associated with "classical" information science (e.g., bibliometrics, information retrieval), editor Blaise Cronin is selectively expanding its footprint in an effort to connect information science more tightly with cognate academic and professional communities.

Knowledge Discovery In Bioinformatics

Author: Xiaohua Hu
Publisher: John Wiley & Sons
ISBN: 9780470124635
Size: 38.16 MB
Format: PDF, ePub, Docs
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The purpose of this edited book is to bring together the ideas and findings of data mining researchers and bioinformaticians by discussing cutting-edge research topics such as, gene expressions, protein/RNA structure prediction, phylogenetics, sequence and structural motifs, genomics and proteomics, gene findings, drug design, RNAi and microRNA analysis, text mining in bioinformatics, modelling of biochemical pathways, biomedical ontologies, system biology and pathways, and biological database management.

Perl For Exploring Dna

Author: Mark D. LeBlanc
Publisher: Oxford University Press on Demand
ISBN:
Size: 68.20 MB
Format: PDF, ePub, Docs
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This book provides an exceptionally friendly introduction to Perl that emphasizes good programming practices with repeated exposure to pattern matching as applied to biological sequence analysis (DNA analysis, Protein analysis). The full-length book is appropriate for postgraduates in either computer science or biology and especially relevant to new interdisciplinary courses involving students from multiple disciplines.

Mastering Perl For Bioinformatics

Author: James Tisdall
Publisher: "O'Reilly Media, Inc."
ISBN: 9781449390907
Size: 46.26 MB
Format: PDF
View: 3467
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Historically, programming hasn't been considered a critical skill for biologists. But now, with access to vast amounts of biological data contained in public databases, programming skills are increasingly in strong demand in biology research and development. Perl, with its highly developed capacities in string handling, text processing, networking, and rapid prototyping, has emerged as the programming language of choice for biological data analysis.Mastering Perl for Bioinformatics covers the core Perl language and many of its module extensions, presenting them in the context of biological data and problems of pressing interest to the biological community. This book, along with Beginning Perl for Bioinformatics, forms a basic course in Perl programming. This second volume finishes the basic Perl tutorial material (references, complex data structures, object-oriented programming, use of modules--all presented in a biological context) and presents some advanced topics of considerable interest in bioinformatics.The range of topics covered in Mastering Perl for Bioinformatics prepares the reader for enduring and emerging developments in critical areas of bioinformatics programming such as: Gene finding String alignment Methods of data storage and retrieval (SML and databases) Modeling of networks (graphs and Petri nets) Graphics (Tk) Parallelization Interfacing with other programming languages Statistics (PDL) Protein structure determination Biological models of computation (DNA Computers) Biologists and computer scientists who have conquered the basics of Perl and are ready to move even further in their mastery of this versatile language will appreciate the author's well-balanced approach to applying Perl's analytical abilities to the field of bioinformatics. Full of practical examples and real-world biological problem solving, this book is a must for any reader wanting to move beyond beginner level Perl in bioinformatics.