Over the last years a great number of bacterial genomes were sequenced. Now one of the most important challenges of\ncomputational genomics is the functional annotation of nucleic acid sequences. In this study we presented the computational\nmethod and the annotation system for predicting biological functions using phylogenetic profiles. The phylogenetic profile of a\ngene was created by way of searching for similarities between the nucleotide sequence of the gene and 1204 reference genomes,\nwith further estimation of the statistical significance of found similarities. The profiles of the genes with known functions were\nused for prediction of possible functions and functional groups for the new genes. We conducted the functional annotation for\ngenes from 104 bacterial genomes and compared the functions predicted by our system with the already known functions. For the\ngenes that have already been annotated, the known function matched the function we predicted in 63% of the time, and in 86% of\nthe time the known function was found within the top five predicted functions. Besides, our system increased the share of annotated\ngenes by 19%. The developed system may be used as an alternative or complementary system to the current annotation systems
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