Genome analysis without compare

Method measures selection pressures on a single genome without use of comparative genomics

David Secko(dmsecko@interchange.ubc.ca)
Apr 27, 2004

A report in the April 29 Nature describes a novel method for detecting selection pressures on specific proteins using a single genome rather than comparing nucleotide sequences.

Measurement of selection pressure on proteins classically involves the comparison of nucleotide sequences from numerous individuals or species, requiring numerous homologous sequences. This approach can be limited by lack of suitable homologs, unfeasibility of sequencing additional genomes, or proteins lacking recognizable homologs.

“The article describes a new way to analyze DNA sequences to identify all of the genes in a genome that are under pressure both to evolve and not to evolve. The advantage here is that by just taking a single genome you're interested in and looking at that sequence, you can find a hidden footprint without comparing homologous genes,” said Joshua Plotkin, from the Bauer Center for Genomics Research and lead author of the study.

The method relies on a...