1 Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark2 Department of Systems Biology, Technical University of Denmark3 unknown4 Department of Bio and Health Informatics, Technical University of Denmark5 Comparative Microbial Genomics, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark6 Department of Chemistry, Technical University of Denmark
In sequenced microbial genomes, some of the annotated genes are actually not protein-coding genes, but rather open reading frames that occur by chance. Therefore, the number of annotated genes is higher than the actual number of genes for most of these microbes. Comparison of the length distribution of the annotated genes with the length distribution of those matching a known protein reveals that too many short genes are annotated in many genomes. Here we estimate the true number of protein-coding genes for sequenced genomes. Although it is often claimed that Escherichia coli has about 4300 genes, we show that it probably has only similar to 3800 genes, and that a similar discrepancy exists for almost all published genomes.
Trends in Genetics, 2001, Vol 17, Issue 8, p. 425-428