Resumo de Beginning Perl For Bioinformatics

This book shows biologists with little or no programming experience howto use Perl, the ideal language for biological data analysis. Eachchapter focuses on solving a particular problem or class of problems,so you'll finish the book with a solid understanding of Perl basics, acollection of programs for such tasks as parsing BLAST and GenBank, andthe skills to tackle more advanced bioinformatics programming. Biology, itseems, is a good showcase for the talents of Perl. Newcomers to Perlwho understand biological information will find James Tisdall's Beginning Perl for Bioinformaticsto be an excellent compendium of examples. Teachers of Perl willlikewise find the text to be filled with fresh programmingillustrations of growing scientific importance. Seasoned Perlmongerswho want to learn biology, however, should search elsewhere, asTisdall's emphasis is on Perl's logic rather than Mother Nature's. Departing from O'Reilly's earlier monograph Developing Bioinformatic Computer Skills,Tisdall's text is organized aggressively along didactic lines. Nearlyall of the 13 chapters begin with twin bullet lists of Perl programmingtools and the bioinformatic methods that require them. Likewise, thechapters end with exercises. String concatenation is illustrated withgene splicing, and regular expressions are taught with genetranscription and motif searching. Tisdall emphasizes sequenceexamples throughout, leading up to an introduction to a Perl interfacefor the NIH GenBank biological database and the widely used BLASTsequence alignment tool. After a brief discussion of three-dimensionalprotein structure, he returns to sequence extraction and secondarystructure prediction. Tisdall's goal is to boost the beginningprogrammer into a domain of self-learning. He imparts essentialetiquette for the success of programming newbies: use the wealth orresources available, from user documentation to Web site surveys toFAQs to How-To's to news groups and finally to direct personal appealsfor help from a senior colleague. A well-plugged-in bioinformatics Perlstudent will soon discover Bioperl, an open-source effort to bringresearch-grade bioinformatic tools to the Perl community. Bioperl isdescribed briefly at the end of Tisdall's book and will reportedly be aforthcoming title of its own in the O'Reilly bioinformatics series.Although he introduces bioinformatics as an academic discipline,Tisdall treats it as a trade throughout his book. He indicates thatopen questions and computational hard problems exist, but does notdescribe what they are or how they are being tackled. Ultimately,Tisdall presents bioinformatics as another arrow in a bench scientist'squiver, very much like HPLC, 2D-PAGE, and the various spectroscopies.As odd as a "bioinformatics-as-tool" book may be to its researchproponents, the reduction of bioinformatics to trade status bothdeflates and vindicates the years of research, as Tisdall's workattests. --Peter Leopold Book Description With its highly developedcapacity to detect patterns in data, Perl has become one of the mostpopular languages for biological data analysis. But if you're abiologist with little or no programming experience, starting out inPerl can be a challenge. Many biologists have a difficult time learninghow to apply the language to bioinformatics. The most popular Perlprogramming books are often too theoretical and too focused on computerscience for a non-programming biologist who needs to solve veryspecific problems. Beginning Perl for Bioinformaticsis designed to get you quickly over the Perl language barrier byapproaching programming as an important new laboratory skill, revealingPerl programs and techniques that are immediately useful in the lab.Each chapter focuses on solving a particular bioinformatics problem orclass of problems, starting with the simplest and increasing incomplexity as the book progresses. Each chapter includes programmingexercises and teaches bioinfious kinds of practical biologBy theend of the book you'll have a solid understanding of Perl basics, acollection of programs for such tasks as parsing BLAST and GenBank, andthe skills to take on more advanced bioinformatics programming. Some ofthe later chapters focus in greater detail on specific bioinformaticstopics. This book is suitable for use as a classroom textbook, forself-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 Book Info Designed to get you quickly overthe Perl language barrier by approaching programming as an importantnew laboratory skill revealing Perl programs and techniques that areimmediately useful in the lab. Softcover.

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