Analysis of the Thermotoga maritima genome combining a variety of sequencesimilarity and genome context tools

The proliferation of genome sequence data has led to the development of a n umber of tools and strategies that facilitate computational analysis. These methods include the identification of motif patterns, membership of the qu ery sequences in family databases, metabolic pathway involvement and gene p roximity, We re-examined the completely sequenced genome of Thermotoga mari tima by employing the combined use of the above methods, By analyzing all 1 877 proteins encoded in this genome, we identified 193 cases of conflicting annotations (10%), of which 164 are new function predictions and 29 are am endments of previously proposed assignments, These results suggest that the combined use of existing computational tools can resolve inconclusive sequ ence similarities and significantly improve the prediction of protein funct ion from genome sequence.