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Beginning Perl for Bioinformatics by James Tisdall

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Perl's Benefits

The following sections illustrate some of Perl's strong points.

Ease of Programming

Computer languages differ in which things they make easy. By "easy" I mean easy for a programmer to program. Perl has certain features that simplifies several common bioinformatics tasks. It can deal with information in ASCII text files or flat files, which are exactly the kinds of files in which much important biological data appears, in the GenBank and PDB databases, among others. (See the discussion of ASCII in Chapter 4; GenBank and PDB are the subjects in Chapter 10 and Chapter 11.) Perl makes it easy to process and manipulate long sequences such as DNA and proteins. Perl makes it convenient to write a program that controls one or more other programs. As a final example, Perl is used to put biology research labs, and their results, on their own dynamic web sites. Perl does all this and more.

Although Perl is a language that's remarkably suited to bioinformatics, it isn't the only choice nor is it always the best choice. Other programming languages such as C and Java are also used in bioinformatics. The choice of language depends on the problem to be programmed, the skills of the programmers, and the available system.

Rapid Prototyping

Another important benefit of using Perl for biological research is the speed with which a programmer can write a typical Perl program (referred to as rapid prototyping). Many problems can be solved in far fewer lines of Perl code than in C or Java. ...

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