Gene Prediction Using Computers

When the complete mRNA sequence for a gene is known, computer programs are used to align the mRNA sequence with the appropriate region of the genomic DNA sequence. This provides a reliable indication of the beginning and end of the coding region for that gene. In the absence of a complete mRNA sequence, the boundaries can be estimated by ever-improving, but still inexact, gene prediction software. The problem is the lack of a single sequence pattern that indicates the beginning or end of a eukaryotic gene. Fortunately, the middle of a gene, referred to as the core gene sequence--has enough consistent features to allow more reliable predictions.