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Beginning Perl for Bioinformatics by James Tisdall

By James Tisdall

With its hugely built means to observe styles in information, Perl has turn into probably the most renowned 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 by means of impending programming as a major new laboratory ability, revealing Perl courses and strategies which are instantly valuable within the lab. every one bankruptcy specializes in fixing a selected bioinformatics challenge or classification of difficulties, beginning with the best and extending in complexity because the publication progresses. each one bankruptcy contains programming workouts. by means of the top of the booklet you'll have a great figuring out of Perl fundamentals, a suite of courses for such projects as parsing BLAST and GenBank, and the abilities to tackle extra complicated bioinformatics programming.

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Pseudocode is not Perl code, so the Perl interpreter will complain about any pseudocode that is not commented out. You can comment out the pseudocode by placing # signs at the beginning of all pseudocode lines: #get the name of DNAfile from the user #read in the DNA from the DNAfile #for each regulatory element # if element is in DNA, then # add one to the count IT-SC 37 #print count As you expand your pseudocode design into Perl code, you can uncomment the Perl code by removing the # signs. In this way you may have a mixture of Perl and pseudocode, but you can run and test the Perl parts; the Perl interpreter simply ignores commented-out lines.

The data your program uses to compute is called the input . Input can come from files, from other programs, from users running the program, from forms filled out on web sites, from email messages, and so forth. Most programs read in some form of input; some programs don't. Let's add the list of regulatory elements to the actual program code. You can ask for a file that contains this list, as we did with the DNA, and have the program be capable of searching different lists of regulatory elements.

Finally, just to exercise the different parts of the language, let's accomplish the same concatenation using only the print statement: print $DNA1, $DNA2, "\n"; Here the print statement has three parts, separated by commas: the two DNA fragments in the two variables and a newline. " Before leaving this section, let's look ahead to other uses of Perl variables. You've seen the use of variables to hold strings of DNA sequence data. There are other types of data, and programming languages need variables for them, too.

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