Reading Genomes Like Books

Comparing whole genome sequences of different organisms to construct their evolutionary trees can be very tedious and time consuming. Scientists use techniques that rely on the comparison of small sets of genes that the organisms being compared have in common. These methods, however, might not be applicable when comparing distantly related organisms. Inspired by the text comparison methods used to detect plagiarism in computer programs, books and other publications, a team of researchers from University of California, Berkeley developed an improved method for comparing whole genome sequences.

“The method treats the genome like a book without spaces,” said Sung-Hou Kim lead researcher of the study. Kim noted that the method, called FFP, produces groupings of organisms largely consistent with current groupings but with some discrepancies. For instance, the relative positions of the groups in the family tree are quite different from those based on conventional gene alignment methods.

In addition to its application in comparative genomics, Kim expects that FFP will help in tracing human ancestry and disease demography, as well as in grouping metagenomic data. The paper appears this week in the early online edition of the journal Proceedings of the National Academy of Sciences.

The complete article is available at http://www.berkeley.edu/news/media/releases/2009/01/28_genomecomp.shtml