Finding genes by computer: the state of the art

Discovering new genes, and their functions, can be aided not only by special purpose gene (and coding region) finding software, but also by searches in key databases, and by programs for finding particular sites relevant to gene expression, such as promoters and splice sites. No one software package includes all the necessary tools. I describe here the main kinds of tools; their working principles, strengths and limitations; and how combined evidence from multiple tools can aid in optimum gene identification.