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Genomic Perl

Author: Rex A. Dwyer
Publisher: Cambridge University Press
ISBN: 9780521801775
Size: 25.65 MB
Format: PDF, Kindle
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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: 60.32 MB
Format: PDF, ePub
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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.

Basic Bioinformatics

Author: S. Ignacimuthu
Publisher: Alpha Science Int'l Ltd.
ISBN: 9781842652312
Size: 52.84 MB
Format: PDF, ePub, Mobi
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Bioinformatics is a computer-assisted interface discipline dealing with acquisition, storage, management, access and processing of biological data. This book provides the newcomer enough information to understand the principles of bioinformatic applications covers: History and Importance of Bioinformatics, DNA, RNA and Protein, and Databases.

Annual Review Of Information Science And Technology

Author: Blaise Cronin
Publisher: Information Today, Inc.
ISBN: 9781573872096
Size: 54.51 MB
Format: PDF, ePub, Docs
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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: 46.31 MB
Format: PDF
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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.

Beginning Perl For Bioinformatics

Author: James Tisdall
Publisher: "O'Reilly Media, Inc."
ISBN: 9780596550479
Size: 61.74 MB
Format: PDF, Kindle
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With its highly developed capacity to detect patterns in data, Perl has become one of the most popular languages for biological data analysis. But if you're a biologist with little or no programming experience, starting out in Perl can be a challenge. Many biologists have a difficult time learning how to apply the language to bioinformatics. The most popular Perl programming books are often too theoretical and too focused on computer science for a non-programming biologist who needs to solve very specific problems.Beginning Perl for Bioinformatics is designed to get you quickly over the Perl language barrier by approaching programming as an important new laboratory skill, revealing Perl programs and techniques that are immediately useful in the lab. Each chapter focuses on solving a particular bioinformatics problem or class of problems, starting with the simplest and increasing in complexity as the book progresses. Each chapter includes programming exercises and teaches bioinformatics by showing and modifying programs that deal with various kinds of practical biological problems. By the end of the book you'll have a solid understanding of Perl basics, a collection of programs for such tasks as parsing BLAST and GenBank, and the skills to take on more advanced bioinformatics programming. Some of the later chapters focus in greater detail on specific bioinformatics topics. This book is suitable for use as a classroom textbook, for self-study, and as a reference.The book covers: Programming basics and working with DNA sequences and strings Debugging your code Simulating gene mutations using random number generators Regular expressions and finding motifs in data Arrays, hashes, and relational databases Regular expressions and restriction maps Using Perl to parse PDB records, annotations in GenBank, and BLAST output

Genomics And Bioinformatics

Author: Tore Samuelsson
Publisher: Cambridge University Press
ISBN: 1107378338
Size: 49.35 MB
Format: PDF, ePub, Docs
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With the arrival of genomics and genome sequencing projects, biology has been transformed into an incredibly data-rich science. The vast amount of information generated has made computational analysis critical and has increased demand for skilled bioinformaticians. Designed for biologists without previous programming experience, this textbook provides a hands-on introduction to Unix, Perl and other tools used in sequence bioinformatics. Relevant biological topics are used throughout the book and are combined with practical bioinformatics examples, leading students through the process from biological problem to computational solution. All of the Perl scripts, sequence and database files used in the book are available for download at the accompanying website, allowing the reader to easily follow each example using their own computer. Programming examples are kept at an introductory level, avoiding complex mathematics that students often find daunting. The book demonstrates that even simple programs can provide powerful solutions to many complex bioinformatics problems.

Perl For Exploring Dna

Author: Mark D. LeBlanc
Publisher: Oxford University Press on Demand
ISBN:
Size: 72.75 MB
Format: PDF, ePub
View: 6499
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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.