Novel coding regions in four complete archaeal genomes

In the process of analysing the four available complete archaeal genomes, w e have noted that certain regions characterised as 'non-coding' exhibit sig nificant sequence similarity to other protein sequences from Archaea and ot her species. Using established technology, we have identified a number of p otential protein coding regions in these putative 'non-coding' regions. We have detected 524 such cases, of which 113 regions appear to code for prote ins present in archaeal or other species, while the remaining 411 regions a re mostly start/stop definition conflicts. Of the 113 protein coding region s, only 21 code for proteins with homologues of known function. The number of novel coding sequences identified herein amounts to 1.5% of the total ge nome entries, while the conflicting cases represent an additional 5%. The o bserved differences between the four complete archaeal genomes seem to refl ect disparate approaches to genome annotation. Genome sequence collections should be regularly checked to improve gene prediction by sequence similari ty and greater effort is required to make gene definitions consistent acros s related species.