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Scientists develop new method to investigate origin of life
Date:9/2/2008

nary histories of retroelements. Their method uses a computer algorithm to generate evolutionary profiles -- also called phylogenetic profiles -- that are compared all-against-all. For example, given four sequences, the new method compares profile A to profiles B, C, and D; it compares profile B to profiles C and D; and so on, for a total of six comparisons. The method then selects the regions of the profiles that match and creates a tree-like diagram, called a phylogenetic tree, based on the retroelements' similarities to one another. The tree provides evolutionary distance estimates and, hence, phylogenetic relationships among retroelements. Patterson said that the results from this study help to clarify many existing theories on retroelement evolution.

The conventional method for estimating evolutionary relationships, called multiple sequence alignment, also produces evolutionary trees, but can be insensitive to relationships among the most distantly related proteins, in large part because it makes only one simultaneous comparison across all of the genetic/protein sequences. To obtain more detailed information about possible relationships among the sequences, a human expert who can manually search for such relationships is needed. But Patterson said that relying on humans to do the work is not ideal.

"Although the human mind is the most powerful tool for pattern recognition, human-based measurements often are hard to reproduce," he said. "For example, if you do something and I do something, we're going to do it differently. It's better to have a standardized method for gauging relationships among ancient proteins, and that's exactly what we've created." According to Damian van Rossum, Penn State research associate/assistant professor of biology and another leader on the project, the new method can be used in conjunction with the conventional method to get a clearer picture of the evolutionary histories of proteins. "The more independe
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Contact: Barbara K. Kennedy
science@psu.edu
818-633-4682
Penn State
Source:Eurekalert  

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Scientists develop new method to investigate origin of life
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