Computational Gene nding

Computational methodology for nding genes and other functional sites in genomic DNA has evolved signi cantly over the last 20 years. Excellent recent surveys have been given by Gelfand [27], Fickett [20, 21], Guig o [31], Claverie [13], Milanesi and Rogosin [50], and Krogh [41]. Extensive bibliographies are available at http://linkage.rockefeller.edu/wli/gene/ and http://www-hto.usc.edu/software/procrustes/fans_ref/. Here we give only a very brief overview. Among the types of functional sites in genomic DNA that researchers have sought to recognize are splice sites, start and stop codons, branch points, promoters and terminators of transcription, polyadenylation sites, ribosomal binding sites, topoisomerase II binding sites, topoisomerase I cleavage sites, and various transcription factor binding sites [27]. Local sites such as these are called signals and methods for detecting them may be called signal sensors. Genomic DNA signals can be contrasted with extended and variable length regions such as exons and introns, which are recognized by di erent methods that may be called content sensors [64, 65].