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Beginning Perl For Bioinformatics

Author: James Tisdall
Publisher: "O'Reilly Media, Inc."
ISBN: 9780596550479
Size: 33.32 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

Beginning Perl For Bioinformatics

Author: James Tisdall
Publisher: "O'Reilly Media, Inc."
ISBN: 0596000804
Size: 77.29 MB
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Discusses the ties between biology and computer science, how to program, basic PERL programming concepts, and how to use PERL to perform tasks including analyzing genetic codes.

Mastering Perl For Bioinformatics

Author: James Tisdall
Publisher: "O'Reilly Media, Inc."
ISBN: 9781449390907
Size: 17.76 MB
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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.

Perl Programming For Biologists

Author: D. Curtis Jamison
Publisher: John Wiley & Sons
ISBN: 9780471430599
Size: 67.22 MB
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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.

Bioinformatics Programming Using Python

Author: Mitchell L Model
Publisher: "O'Reilly Media, Inc."
ISBN: 9781449382902
Size: 36.60 MB
Format: PDF, Kindle
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Powerful, flexible, and easy to use, Python is an ideal language for building software tools and applications for life science research and development. This unique book shows you how to program with Python, using code examples taken directly from bioinformatics. In a short time, you'll be using sophisticated techniques and Python modules that are particularly effective for bioinformatics programming. Bioinformatics Programming Using Python is perfect for anyone involved with bioinformatics -- researchers, support staff, students, and software developers interested in writing bioinformatics applications. You'll find it useful whether you already use Python, write code in another language, or have no programming experience at all. It's an excellent self-instruction tool, as well as a handy reference when facing the challenges of real-life programming tasks. Become familiar with Python's fundamentals, including ways to develop simple applications Learn how to use Python modules for pattern matching, structured text processing, online data retrieval, and database access Discover generalized patterns that cover a large proportion of how Python code is used in bioinformatics Learn how to apply the principles and techniques of object-oriented programming Benefit from the "tips and traps" section in each chapter

Developing Bioinformatics Computer Skills

Author: Cynthia Gibas
Publisher: "O'Reilly Media, Inc."
ISBN: 9781565926646
Size: 19.94 MB
Format: PDF
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Offers a structured approach to biological data and the computer tools needed to analyze it, covering UNIX, databases, computation, Perl, data mining, data visualization, and tailoring software to suit specific research needs.

Beginning Perl

Author: Curtis Poe
Publisher: John Wiley & Sons
ISBN: 1118235630
Size: 80.63 MB
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Everything beginners need to start programming with Perl Perl is the ever-popular, flexible, open source programming language that has been called the programmers’ Swiss army knife. This book introduces Perl to both new programmers and experienced ones who are looking to learn a new language. In the tradition of the popular Wrox Beginning guides, it presents step-by-step guidance in getting started, a host of try-it-out exercises, real-world examples, and everything necessary for a Perl novice to start programming with confidence. Introduces Perl to both new programmers and experienced ones who want to learn a new language Provides a host of real-world applications for today's environments so readers can get started immediately Covers the new features of Perl but fully applicable to previous editions Beginning Perl provides the information and instruction you need to confidently get started with Perl. For Instructors: Classroom and training support material are available for this book.

Bioinformatics And Functional Genomics

Author: Jonathan Pevsner
Publisher: John Wiley & Sons
ISBN: 1118581784
Size: 46.28 MB
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Bioinformatics and Functional Genomics, Third Edition is the latest revision of this bestselling and indispensible text book. Thoroughly updated to encompass the latest advances in the field the book retains its broad and accessible approach. Divided into three parts the book deals first with bioinformatics, the use of computer databases and computer algorithms in the study of proteins and genes. The first section includes sequence alignment, database searches and phylogeny. The second section of the book focuses on functional genomics and includes approaches such as gene expression profiling and proteomics that are used to study cellular function. The final part of the book deals with genomics which is the study of the collection of DNA that comprises an organism, using the tools of bioinformatics. Bioinformatics and Functional Genomics, Third Edition will serve as an excellent single-source textbook for advanced undergraduate and beginning graduate-level courses in the biological sciences and computer sciences. It will also provide an essential resource for biologists in a broad variety of disciplines who use the tools of bioinformatics and genomics to study particular research problems; bioinformaticists and computer scientists who develop computer algorithms and databases; and medical researchers and clinicians who want to understand the genomic basis of viral, bacterial, parasitic, or other diseases.

Genomics And Bioinformatics

Author: Tore Samuelsson
Publisher: Cambridge University Press
ISBN: 1107378338
Size: 76.69 MB
Format: PDF, 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.