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Beginning Perl For Bioinformatics

Author: James Tisdall
Publisher: "O'Reilly Media, Inc."
ISBN: 9780596550479
Size: 44.75 MB
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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

Mastering Perl For Bioinformatics

Author: James Tisdall
Publisher: "O'Reilly Media, Inc."
ISBN: 9781449390907
Size: 32.57 MB
Format: PDF, Docs
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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.

Bioinformatics For Geneticists

Author: Michael R. Barnes
Publisher: John Wiley & Sons
ISBN: 0470026197
Size: 15.51 MB
Format: PDF, ePub
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Bioinformatics for geneticists describes the key bioinformatics and genetic analysis processes that are needed to identify human genetic determinants. Including SNP functional analysis and statistical genetics.

Perl Programming For Bioinformatics

Author: Harshawardhan P. Bal
Publisher: Tata McGraw-Hill Education
ISBN: 9780070474475
Size: 61.59 MB
Format: PDF, ePub
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This book introduces Bioinformatics and its tools and techniques to a new hybrid professional the biologist and the would-be informatician and encourages to use this vast and powerful resource to address biological problems.

Bioinformatics Biocomputing And Perl

Author: Michael Moorhouse
Publisher: John Wiley & Sons
ISBN: 0470026456
Size: 46.66 MB
Format: PDF, Kindle
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Bioinformatics, Biocomputing and Perl presents a modern introduction to bioinformatics computing skills and practice. Structuring its presentation around four main areas of study, this book covers the skills vital to the day-to-day activities of today’s bioinformatician. Each chapter contains a series of maxims designed to highlight key points and there are exercises to supplement and cement the introduced material. Working with Perl presents an extended tutorial introduction to programming through Perl, the premier programming technology of the bioinformatics community. Even though no previous programming experience is assumed, completing the tutorial equips the reader with the ability to produce powerful custom programs with ease. Working with Data applies the programming skills acquired to processing a variety of bioinformatics data. In addition to advice on working with important data stores such as the Protein DataBank, SWISS-PROT, EMBL and the GenBank, considerable discussion is devoted to using bioinformatics data to populate relational database systems. The popular MySQL database is used in all examples. Working with the Web presents a discussion of the Web-based technologies that allow the bioinformatics researcher to publish both data and applications on the Internet. Working with Applications shifts gear from creating custom programs to using them. The tools described include Clustal-W, EMBOSS, STRIDE, BLAST and Xmgrace. An introduction to the important Bioperl Project concludes this chapter and rounds off the book.

Genomics And Bioinformatics

Author: Tore Samuelsson
Publisher: Cambridge University Press
ISBN: 1107008565
Size: 25.34 MB
Format: PDF, ePub
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A hands-on introduction to Unix, Perl and other bioinformatics tools using relevant and interesting molecular biology problems.

Building Bioinformatics Solutions

Author: Conrad Bessant
Publisher: OUP Oxford
ISBN: 0191643203
Size: 48.51 MB
Format: PDF
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Bioinformatics encompasses a broad and ever-changing range of activities involved with the management and analysis of data from molecular biology experiments. Despite the diversity of activities and applications, the basic methodology and core tools needed to tackle bioinformatics problems is common to many projects. This unique book provides an invaluable introduction to three of the main tools used in the development of bioinformatics software - Perl, R and MySQL - and explains how these can be used together to tackle the complex data-driven challenges that typify modern biology. These industry standard open source tools form the core of many bioinformatics projects, both in academia and industry. The methodologies introduced are platform independent, and all the examples that feature have been tested on Windows, Linux and Mac OS. Building Bioinformatics Solutions is suitable for graduate students and researchers in the life sciences who wish to automate analyses or create their own databases and web-based tools. No prior knowledge of software development is assumed. Having worked through the book, the reader should have the necessary core skills to develop computational solutions for their specific research programmes. The book will also help the reader overcome the inertia associated with penetrating this field, and provide them with the confidence and understanding required to go on to develop more advanced bioinformatics skills.

Genomic Perl

Author: Rex A. Dwyer
Publisher: Cambridge University Press
ISBN: 9780521801775
Size: 72.17 MB
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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.

Games Diversions Perl Culture

Author: Jon Orwant
Publisher: "O'Reilly Media, Inc."
ISBN: 9781449397784
Size: 67.76 MB
Format: PDF, Kindle
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The Perl Journal (TPJ) did something most print journals aspire to, but few succeed. Within a remarkable short time, TPJ acquired a cult-following and became the voice of the Perl community. Every serious Perl programmer subscribed to it, and every notable Perl guru jumped at the opportunity to write for it. Back issues were swapped like trading cards. No longer in print format, TPJ remains the quintessential spirit of Perl--a publication for and by Perl programmers who see fun and beauty in an admittedly quirky little language.Games, Diversions, and Perl Culture is the third volume of The Best of the Perl Journal, compiled and re-edited by the original editor and publisher of The Perl Journal, Jon Orwant. In this series, we've taken the very best (and still relevant) articles published in TPJ over its 5 years of publication and immortalized them into three volumes.The 47 articles included in this volume are simply some of the best Perl articles ever written on the subjects of games, diversions, and the unique culture of this close-knit community, by some of the best Perl authors and coders. Games, Diversions & Perl Culture focuses on entertaining topics that make Perl users such fanatics about the language. You'll find all of the playful features TPJ offered over the years, including the Obfuscated Perl Contests, Perl Quiz Shows, humor articles, and renowned one-line recipes. The book also contains a panoply of quirky applications of Perl, including genetic algorithms, home automation, music programming, and an entire section on natural language processing.This anthology is an unmatched compendium of Perl lore.

Perl Programming For Biologists

Author: D. Curtis Jamison
Publisher: John Wiley & Sons
ISBN: 9780471430599
Size: 10.24 MB
Format: PDF
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Working on the assumption that the reader has no formal training in programming, Perl Programming for Biologists demonstrates how Perl is used to solve biological problems. Each chapter opens with a set of learning objectives, provides numerous review questions and self-study exercises, and concludes with a bulleted summary of key points. The author incorporates numerous real-life examples throughout the text. Upon completing the book, readers are able to quickly perform such tasks as correcting recurring errors in spreadsheets, scanning a Fasta sequence for every occurrence of an EcoRI site, adapting other writers' scripts to one's own purposes, and most important, writing reusable and maintainable scripts that spare the rote repetition of code.