Furthermore, the most rapidly evolving genes will not be included in the analysis as many of them will not have detectable orthologs even in closely related genomes.
Tests on a whole genome To test QRNA performance in a realistic whole genome screen, we used it to analyze the Escherichia coli genome by comparisons to the related genome of Salmonella typhi .
It also uses a second related genome to improve the prediction accuracy of the model.
One obvious application is to use this tool as a step in the characterization of an "alphabet" of putatively essential "core" genes in a set of closely related genomes such as from a collection of poxvirus genomes ( unpublished data ).
It has been observed that the genomic signature of phylogenetically related genomes is similar.
The ability to examine further why some genes are retained and some are lost will be improved as additional closely related genomes of different sizes are sequenced and annotated.
The manual inspection of the sequences found with the CM using Infernal allowed finding 38 true homologues in phylogenetically related α-proteobacterial genomes.
Hence, though the differences in content between closely related genomes have been extensively cited as evidence for constant exchanges with distant relatives, these sequences carry no evidence for such exchanges.
Conclusions Buchnera provides the first case of a fully sequenced, highly reduced genome for which closely related large genomes exist and have been sequenced, allowing reconstruction of the steps in genome reduction.
The chromosomal proximity method aims to detect local functional dependences ('intracluster' dependences) established by conserved proximity among distantly related genomes.
