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Computational Methods of Identifying Novel sRNA Genes in E. coli

Introduction: Despite the fact that the existence of sRNAs has been known for some time, most gene identification methods and programs are geared to find only genes that code for proteins, and are incapable of finding genes whose functional form is the RNA itself. It is only recently, with the explosion of identified sRNA genes and the belief that many more exist, that concerted efforts are being made to develop methods that can identify all of the sRNA genes in the genome sequences available, much as has been done (to a certain extent) with protein coding gene-finding algorithms. However, developing accurate computational methods of whole genome scale sRNA gene finding has proven difficult, for a variety of reasons (Eddy, 2001).