Chapter 4. Sequences and Strings

In this chapter you will begin to write Perl programs that manipulate biological sequence data, that is, DNA and proteins. Once you have the sequences in the computer, you'll start writing programs that do the following with the sequence data:

• Transcribe DNA to RNA

• Concatenate sequences

• Make the reverse complement of sequences

• Read sequence data from files

You'll also write programs that give information about your sequences. How GC-rich is your DNA? How hydrophobic is your protein? You'll see programming techniques you can use to answer these and similar questions.

The Perl skills you will learn in this chapter involve the basics of the language. Here are some of those basics:

• Scalar variables

• Array variables

• String operations such as substitution and translation

• Reading data from files