Exon Detection by Similarity Searches

Other chapters of this volume have presented the various experimental methods (mainly exon trapping and recombination-based and hybridization-based approaches) used for the identification of transcribed sequences within cloned genomic fragments. None of those methods require detailed sequence information on the genomic region of interest. However, since generating large genomic sequences is becoming more routine, identifying transcribed regions by computer analysis of large genomic sequence (i.e., “software trapping”) is also becoming a viable alternative. After an overview of the various computational methods at hand, this chapter focuses on the use of database similarity searches for the identification of exons in mammalian genomes.