With the development of genomics and proteomics, many biologists now need to handle large amounts of data for their research. Bioinformatics programming, especially Perl programming, is a well-suited tool for biological data manipulation and analysis. This tutorial will introduce the fundamental concepts and mechanisms of computer programming. We will use practical examples to demonstrate how to write the Perl codes to do transcription, translation, batch sequence retrieval, promoter sequence extraction from genomic DNA, motif scanning, query gene ontology database, etc. Through these examples, you will learn how bioinformatics programming can make your work easier and more efficient.