Figure 2

A basic strategy to look for prokaryotic codingsequence (CDS). A coding sequence is known to start with one Start codon (ATG, GTG or TTG) and ends with a Stop codon (TAA,TAG,TGA) in the same frame (they are separated by a multiple of 3 bases). In-frame Start codons may also appear within the CDS, in which case they code for the methionine. A basic searching strategy therefore consists in first identifying ORFs (Open Reading Frames), i.e. regions which are delimited by two in-frame Stop triplets and long enough to code a protein (typically containing more than 150 bases). The heuristics then searches for the leftmost in-frame Start triplet (i.e. the one yielding the longest predicted CDS). The further discovery of a pattern associated to a ribosome binding site (RBS) upstream of the CDS (usually less than 10 nucleotides before Start) will ascertain this CDS. Conversely, the presence of an RBS inside (but not too far from the beginning) a CDS may lead to the selection of an other Start. Finally, the retrieval of similar sequences in annotated sequence databases may eventually lead the biologist to assert the presence of a coding region. This strategy is given only for illustrative purpose.