Beginning Perl for Bioinformatics

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

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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.

Beginning Perl For Bioinformatics

Beginning Perl For Bioinformatics
Author: James D Tisdall
Publsiher:
Total Pages: 390
Release: 2001-01-01
Genre: Plant diseases
ISBN: 9788173663956

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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.

Beginning Perl for Bioinformatics

Beginning Perl for Bioinformatics
Author: James Tisdall
Publsiher: "O'Reilly Media, Inc."
Total Pages: 386
Release: 2001-10-22
Genre: Computers
ISBN: 0596550472

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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

Mastering Perl for Bioinformatics
Author: James Tisdall
Publsiher: "O'Reilly Media, Inc."
Total Pages: 400
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
Publsiher:
Total Pages:
Release: 2001-01-01
Genre: Computers
ISBN: 9780613911979

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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.

Bioinformatics for Geneticists

Bioinformatics for Geneticists
Author: Michael R. Barnes
Publsiher: John Wiley & Sons
Total Pages: 577
Release: 2007-04-16
Genre: Science
ISBN: 0470026197

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Praise from the reviews: "Without reservation, I endorse this text as the best resource I've encountered that neatly introduces and summarizes many points I've learned through years of experience. The gems of truth found in this book will serve well those who wish to apply bioinformatics in their daily work, as well as help them advise others in this capacity." CIRCGENETICS "This book may really help to get geneticists and bioinformaticians on 'speaking-terms'... contains some essential reading for almost any person working in the field of molecular genetics." EUROPEAN JOURNAL OF HUMAN GENETICS "... an excellent resource... this book should ensure that any researcher's skill base is maintained." GENETICAL RESEARCH “… one of the best available and most accessible texts on bioinformatics and genetics in the postgenome age… The writing is clear, with succinct subsections within each chapter….Without reservation, I endorse this text as the best resource I’ve encountered that neatly introduces and summarizes many points I’ve learned through years of experience. The gems of truth found in this book will serve well those who wish to apply bioinformatics in their daily work, as well as help them advise others in this capacity.” CIRCULATION: CARDIOVASCULAR GENETICS A fully revised version of the successful First Edition, this one-stop reference book enables all geneticists to improve the efficiency of their research. The study of human genetics is moving into a challenging new era. New technologies and data resources such as the HapMap are enabling genome-wide studies, which could potentially identify most common genetic determinants of human health, disease and drug response. With these tremendous new data resources at hand, more than ever care is required in their use. Faced with the sheer volume of genetics and genomic data, bioinformatics is essential to avoid drowning true signal in noise. Considering these challenges, Bioinformatics for Geneticists, Second Edition works at multiple levels: firstly, for the occasional user who simply wants to extract or analyse specific data; secondly, at the level of the advanced user providing explanations of how and why a tool works and how it can be used to greatest effect. Finally experts from fields allied to genetics give insight into the best genomics tools and data to enhance a genetic experiment. Hallmark Features of the Second Edition: Illustrates the value of bioinformatics as a constantly evolving avenue into novel approaches to study genetics The only book specifically addressing the bioinformatics needs of geneticists More than 50% of chapters are completely new contributions Dramatically revised content in core areas of gene and genomic characterisation, pathway analysis, SNP functional analysis and statistical genetics Focused on freely available tools and web-based approaches to bioinformatics analysis, suitable for novices and experienced researchers alike Bioinformatics for Geneticists, Second Edition describes the key bioinformatics and genetic analysis processes that are needed to identify human genetic determinants. The book is based upon the combined practical experience of domain experts from academic and industrial research environments and is of interest to a broad audience, including students, researchers and clinicians working in the human genetics domain.

Building Bioinformatics Solutions

Building Bioinformatics Solutions
Author: Conrad Bessant
Publsiher: OUP Oxford
Total Pages: 352
Release: 2014-01-16
Genre: Science
ISBN: 0191643203

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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.

Genomics and Bioinformatics

Genomics and Bioinformatics
Author: Tore Samuelsson
Publsiher: Cambridge University Press
Total Pages: 357
Release: 2012-06-07
Genre: Computers
ISBN: 1107008565

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A hands-on introduction to Unix, Perl and other bioinformatics tools using relevant and interesting molecular biology problems.

Bioinformatics

Bioinformatics
Author: Thomas Dandekar
Publsiher: Springer Nature
Total Pages: 354
Release: 2023-04-03
Genre: Science
ISBN: 3662650363

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This book offers a gripping introduction to the fastest growing field of biology with easy-to-follow examples and a well-prepared appendix for the reader to cook up and experience everything right away. The book gets the reader started with the basics, such as how to easily find sequence information and then analyze it. In further chapters, the authors go into the various analysis options from RNA, DNA and proteins to entire metabolic pathways. Exciting examples from biology are chosen in each chapter to illustrate the analysis. Each chapter concludes with an exercise section that immediately puts what has been learned to use. The subject of this book is a must for any biology student, whether undergraduate or graduate, as bioinformatics is now unearthing amazing insights into the molecular basis of all living things. Computer science students and other students from related sciences will get a good introduction to bioinformatics, as biology and current topics (e.g. AI) are systematically introduced step by step alongside the software. Discover the key to life together with the authors and learn to understand the language of life. This book is a translation of the original German 2nd edition Bioinformatik by Thomas Dandekar and Meik Kunz, published by Springer-Verlag GmbH Germany, part of Springer Nature in 2021. The translation was done with the help of artificial intelligence (machine translation by the service DeepL.com). A subsequent human revision was done primarily in terms of content, so that the book will read stylistically differently from a conventional translation. Springer Nature works continuously to further the development of tools for the production of books and on the related technologies to support the authors.

Handbook of Hidden Markov Models in Bioinformatics

Handbook of Hidden Markov Models in Bioinformatics
Author: Martin Gollery
Publsiher: CRC Press
Total Pages: 176
Release: 2008-06-12
Genre: Science
ISBN: 1420011804

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Demonstrating that many useful resources, such as databases, can benefit most bioinformatics projects, the Handbook of Hidden Markov Models in Bioinformatics focuses on how to choose and use various methods and programs available for hidden Markov models (HMMs). The book begins with discussions on key HMM and related profile methods, including the HMMER package, the sequence analysis method (SAM), and the PSI-BLAST algorithm. It then provides detailed information about various types of publicly available HMM databases, such as Pfam, PANTHER, COG, and metaSHARK. After outlining ways to develop and use an automated bioinformatics workflow, the author describes how to make custom HMM databases using HMMER, SAM, and PSI-BLAST. He also helps you select the right program to speed up searches. The final chapter explores several applications of HMM methods, including predictions of subcellular localization, posttranslational modification, and binding site. By learning how to effectively use the databases and methods presented in this handbook, you will be able to efficiently identify features of biological interest in your data.

Practical Text Mining with Perl

Practical Text Mining with Perl
Author: Roger Bilisoly
Publsiher: John Wiley & Sons
Total Pages: 296
Release: 2011-09-20
Genre: Computers
ISBN: 1118210506

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Provides readers with the methods, algorithms, and means to perform text mining tasks This book is devoted to the fundamentals of text mining using Perl, an open-source programming tool that is freely available via the Internet (www.perl.org). It covers mining ideas from several perspectives--statistics, data mining, linguistics, and information retrieval--and provides readers with the means to successfully complete text mining tasks on their own. The book begins with an introduction to regular expressions, a text pattern methodology, and quantitative text summaries, all of which are fundamental tools of analyzing text. Then, it builds upon this foundation to explore: Probability and texts, including the bag-of-words model Information retrieval techniques such as the TF-IDF similarity measure Concordance lines and corpus linguistics Multivariate techniques such as correlation, principal components analysis, and clustering Perl modules, German, and permutation tests Each chapter is devoted to a single key topic, and the author carefully and thoughtfully introduces mathematical concepts as they arise, allowing readers to learn as they go without having to refer to additional books. The inclusion of numerous exercises and worked-out examples further complements the book's student-friendly format. Practical Text Mining with Perl is ideal as a textbook for undergraduate and graduate courses in text mining and as a reference for a variety of professionals who are interested in extracting information from text documents.

Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R

Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R
Author: Gabriel Valiente
Publsiher: CRC Press
Total Pages: 368
Release: 2009-04-08
Genre: Science
ISBN: 9781420069747

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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.

XML for Bioinformatics

XML for Bioinformatics
Author: Ethan Cerami
Publsiher: Springer Science & Business Media
Total Pages: 311
Release: 2006-06-02
Genre: Computers
ISBN: 0387274782

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Introduction The goal of this book is to introduce XML to a bioinformatics audience. It does so by introducing the fundamentals of XML, Document Type De?nitions (DTDs), XML Namespaces, XML Schema, and XML parsing, and illustrating these concepts with speci?c bioinformatics case studies. The book does not assume any previous knowledge of XML and is geared toward those who want a solid introduction to fundamental XML concepts. The book is divided into nine chapters: Chapter 1: Introduction to XML for Bioinformatics. This chapter provides an introduction to XML and describes the use of XML in biological data exchange. A bird’s-eye view of our ?rst case study, the Distributed Annotation System (DAS), is provided and we examine a sample DAS XML document. The chapter concludes with a discussion of the pros and cons of using XML in bioinformatic applications. Chapter 2: Fundamentals of XML and BSML. This chapter introduces the fundamental concepts of XML and the Bioinformatic Sequence Markup Language (BSML). We explore the origins of XML, de?ne basic rules for XML document structure, and introduce XML Na- spaces. We also explore several sample BSML documents and visualize these documents in the TM Rescentris Genomic Workspace Viewer.

Computer Science Perl Programming

Computer Science   Perl Programming
Author: Jon Orwant
Publsiher: "O'Reilly Media, Inc."
Total Pages: 760
Release: 2002-11-04
Genre: Computers
ISBN: 1449371353

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In its first five years of existence, The Perl Journal ran 247 articles by over 120 authors. Every serious Perl programmer subscribed to it, and every notable Perl guru jumped at the opportunity to write for it. TPJ explained critical topics such as regular expressions, databases, and object-oriented programming, and demonstrated Perl's utility for fields as diverse as astronomy, biology, economics, AI, and games. The magazine gave birth to both the Obfuscated Perl Contest and the Perl Poetry contest, and remains a proud and timeless achievement of Perl during one of its most exciting periods of development.Computer Science and Perl Programming is the first 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. This volume has 70 articles devoted to hard-core computer science, advanced programming techniques, and the underlying mechanics of Perl.Here's a sample of what you'll find inside: Jeffrey Friedl on Understanding Regexes Mark Jason Dominus on optimizing your Perl programs with Memoization Damian Conway on Parsing Tim Meadowcroft on integrating Perl with Microsoft Office Larry Wall on the culture of Perl Written by 41 of the most prominent and prolific members of the closely-knit Perl community, this anthology does what no other book can, giving unique insight into the real-life applications and powerful techniques made possible by Perl.Other books tell you how to use Perl, but this book goes far beyond that: it shows you not only how to use Perl, but what you could use Perl for. This is more than just The Best of the Perl Journal -- in many ways, this is the best of Perl.

Web Graphics Perl Tk Programming

Web  Graphics   Perl Tk Programming
Author: Jon Orwant
Publsiher: "O'Reilly Media, Inc."
Total Pages: 448
Release: 2003
Genre: Computers
ISBN: 0596003110

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Forty articles from the first five years of "The Perl Journal" discuss web site development, techniques for creating graphics, and using the Perl/TK toolkit for graphical applications.

Bioinformatics Programming Using Python

Bioinformatics Programming Using Python
Author: Mitchell L Model
Publsiher: "O'Reilly Media, Inc."
Total Pages: 528
Release: 2009-12-08
Genre: Computers
ISBN: 9781449382902

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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

Games Diversions Perl Culture

Games  Diversions   Perl Culture
Author: Jon Orwant
Publsiher: "O'Reilly Media, Inc."
Total Pages: 589
Release: 2003-05-22
Genre: Computers
ISBN: 1449397913

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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.