Mastering Perl for Bioinformatics

Mastering Perl for Bioinformatics
Author: James Tisdall
Publisher: "O'Reilly Media, Inc."
Total Pages: 399
Release: 2003-09-25
Genre: Computers
ISBN: 1449390900

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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.

Beginning Perl for Bioinformatics

Beginning Perl for Bioinformatics
Author: James Tisdall
Publisher: "O'Reilly Media, Inc."
Total Pages: 384
Release: 2001
Genre: Computers
ISBN: 0596000804

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This book shows biologists with little or no programming experience how to use Perl, the ideal language for biological data analysis. Each chapter focuses on solving a particular problem or class of problems, so you'll finish the book with the skills to tackle more advanced bioinformatics programming.

Mastering Perl for Bioinformatics

Mastering Perl for Bioinformatics
Author: John Smith
Publisher: Independently Published
Total Pages: 0
Release: 2024-04-27
Genre: Computers
ISBN:

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"Mastering Perl for Bioinformatics" is an essential resource designed to equip researchers, professionals, and students with the Perl programming skills required to tackle the computational challenges of modern biology. Covering fundamental to advanced techniques, this book provides a detailed exploration of how Perl can be employed in the analysis of DNA and RNA, protein sequences, and genomic data, as well as in systems biology and bioinformatics algorithms. Through practical examples, tutorials, and case studies, readers will learn to handle vast biological datasets, develop their own bioinformatics tools, and perform complex analyses. Each chapter dives deep into different aspects of bioinformatics, from basic syntax to the integration of external tools and databases, ensuring that readers can progress from foundational techniques to sophisticated applications seamlessly. Whether you're starting out in computational biology or looking to enhance your data analysis skills, "Mastering Perl for Bioinformatics" offers the comprehensive and accessible guidance necessary to master the tools and methodologies of this crucial science. Gain the Perl expertise to advance your research and unlock new possibilities in biological discovery.

Perl Programming for Biologists

Perl Programming for Biologists
Author: D. Curtis Jamison
Publisher: John Wiley & Sons
Total Pages: 206
Release: 2003-07-14
Genre: Medical
ISBN: 9780471430599

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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.

Learning Perl

Learning Perl
Author: Randal Schwartz
Publisher: "O'Reilly Media, Inc."
Total Pages: 389
Release: 2011-06-23
Genre: Computers
ISBN: 1449303587

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The sixth edition of this bestselling Perl tutorial includes recent changes to the language. Years of classroom testing and experience helped shape the book's pace and scope, and this edition is packed with exercises that let readers practice the concepts while they follow the text.

UNIX and Perl to the Rescue!

UNIX and Perl to the Rescue!
Author: Keith Bradnam
Publisher: Cambridge University Press
Total Pages: 429
Release: 2012-07-19
Genre: Science
ISBN: 1107377773

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Your research has generated gigabytes of data and now you need to analyse it. You hate using spreadsheets but it is all you know, so what else can you do? This book will transform how you work with large and complex data sets, teaching you powerful programming tools for slicing and dicing data to suit your needs. Written in a fun and accessible style, this step-by-step guide will inspire and inform non-programmers about the essential aspects of Unix and Perl. It shows how, with just a little programming knowledge, you can write programs that could save you hours, or even days. No prior experience is required and new concepts are introduced using numerous code examples that you can try out for yourself. Going beyond the basics, the authors touch upon many broader topics that will help those new to programming, including debugging and how to write in a good programming style.

Bioinformatics Biocomputing and Perl

Bioinformatics Biocomputing and Perl
Author: Michael Moorhouse
Publisher: John Wiley & Sons
Total Pages: 506
Release: 2005-09-27
Genre: Medical
ISBN: 0470026456

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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.

Programming Perl in the .NET Environment

Programming Perl in the .NET Environment
Author: Yevgeny Menaker
Publisher: Prentice Hall Professional
Total Pages: 498
Release: 2003
Genre: Electronic books
ISBN: 9780130652065

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A practical introduction to programming in Perl utilizing the rich capabilities of Perl and the services provided by .NET.

Mastering Python for Bioinformatics

Mastering Python for Bioinformatics
Author: Ken Youens-Clark
Publisher: "O'Reilly Media, Inc."
Total Pages: 457
Release: 2021-05-05
Genre: Computers
ISBN: 1098100859

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Life scientists today urgently need training in bioinformatics skills. Too many bioinformatics programs are poorly written and barely maintained--usually by students and researchers who've never learned basic programming skills. This practical guide shows postdoc bioinformatics professionals and students how to exploit the best parts of Python to solve problems in biology while creating documented, tested, reproducible software. Ken Youens-Clark, author of Tiny Python Projects (Manning), demonstrates not only how to write effective Python code but also how to use tests to write and refactor scientific programs. You'll learn the latest Python features and toolsâ??including linters, formatters, type checkers, and testsâ??to create documented and tested programs. You'll also tackle 14 challenges in Rosalind, a problem-solving platform for learning bioinformatics and programming. Create command-line Python programs to document and validate parameters Write tests to verify refactor programs and confirm they're correct Address bioinformatics ideas using Python data structures and modules such as Biopython Create reproducible shortcuts and workflows using makefiles Parse essential bioinformatics file formats such as FASTA and FASTQ Find patterns of text using regular expressions Use higher-order functions in Python like filter(), map(), and reduce()

BLAST

BLAST
Author: Ian Korf
Publisher: "O'Reilly Media, Inc."
Total Pages: 363
Release: 2003-07-29
Genre: Computers
ISBN: 0596002998

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This is the only book completely devoted to the popular BLAST (Basic Local Alignment Search Tool), and one that every biologist with an interest in sequence analysis should learn from.