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Download Beginning Perl for Bioinformatics by James Tisdall PDF

By James Tisdall

With its hugely built ability to realize styles in information, Perl has turn into essentially the most well known languages for organic facts research. but when you're a biologist with very little programming adventure, beginning out in Perl could be a problem. Beginning Perl for Bioinformatics is designed to get you speedy over the Perl language barrier via coming near near programming as a major new laboratory ability, revealing Perl courses and methods which are instantly priceless within the lab. every one bankruptcy makes a speciality of fixing a selected bioinformatics challenge or type of difficulties, beginning with the easiest and lengthening in complexity because the ebook progresses. every one bankruptcy contains programming routines. via the top of the ebook you'll have an exceptional realizing of Perl fundamentals, a set of courses for such initiatives as parsing BLAST and GenBank, and the talents to tackle extra complicated bioinformatics programming.

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Example text

It should be installed on your computer, and it may also be found on the Internet at the Perl site. The Perl documentation may come in slightly different forms on your computer system, but the web version is the same for everybody. That's the version I refer to in this book. See the references in Appendix A for more discussion about different sources of Perl documentation. Just to try it out, let's look up the print operator. com. Then click on the Documentation link. Select "Perl's Builtin Functions" and then "Alphabetical Listing of Perl's Functions".

You find, however, that the program isn't doing what you want it to do. Now you have to go back, look at the program, and try to figure out what's wrong. Perhaps you made a simple mistake, such as adding instead of subtracting. You may have misread the documentation, and you're using the language the wrong way (reread the documentation). You may simply have an inadequate plan for accomplishing your goal (rethink your strategy and reprogram that part of the code). Sometimes you can't see what's wrong, and you have to look elsewhere (try searching newsgroup archives or FAQs or asking colleagues for help).

For instance, this sentence is a string. A language is a (finite or infinite) set of strings. In this book, the languages are mainly DNA and protein sequence data. You often hear bioinformaticians referring to an actual sequence of DNA or protein as a "string," as opposed to its representation as sequence data. This is an example of the terminologies of the two disciplines crossing over into one another. As you've seen in the tables, we'll be representing data as simple letters, just as written on a page.

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