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Date:2/23/2009

Since the sequencing of the human genome eight years ago, enormous progress has been made in analyzing and understanding it. Nevertheless, the function of most human genes is still barely understood. An important first step in determining the function of a gene or protein is to compare its sequence with the sequences of hundreds of other organisms that are experimentally easier to investigate. From the functions of related genes or proteins identified in these database searches, the researchers can often infer the unknown functions of human or animal genes. Now, computational biologists Johannes Soeding and Andreas Biegert of the Gene Center of LMU Munich have successfully developed a method that makes database searches significantly more sensitive, while being just as quick. Instead of comparing sequences letter by letter, their idea is to take the sequence neighbors surrounding each letter into account during the comparison. This idea should be generally applicable in other areas of sequence searching and sequence analysis.

The rule for both genes and proteins is: their function is primarily based on the sequence of their DNA or amino acid components. Genes with similar sequences frequently have a similar function. The same goes for proteins, although for them, the three-dimensional structure into which they fold, and which cannot be predicted offhand from their sequence, is equally important. Still, similar protein sequences suggest relatedness or, in other words, the descent from a common ancestral protein, and with it a similar function.

Accordingly, the sequences and functions of genes and proteins all get stored away into databases, which scientists around the world use for comparing their new data against. But even the best and most frequently used algorithms such as BLAST (Basic Local Alignment Search Tool) have to make use of certain simplifications in order to make efficient searching in the gigantic databases possible at all. After all
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Contact: Luise Dirscherl
dirscherl@lmu.de
49-892-180-2706
Ludwig-Maximilians-Universitt Mnchen
Source:Eurekalert

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