Date:12/25/2011

s of sensitivity. The trick is first to assemble similar sequences from the database into multiple sequence alignments. Each alignment column is then labeled with one of 219 "letters", such that columns with similar amino acid composition are represented by the same letter. "By translating the multiple sequence alignments into sequences composed of these 219 letters, we can replace the time-consuming pairwise comparison of HMMs by the comparison of simple sequences", says Sding. This reduces the search time 2500-fold. Sding emphasizes that "HHblits allows to predict the function and structure of proteins more often and more accurately than was previously possible." His group is already working on further improvements to the method, for example by incorporating information on the three-dimensional structures of proteins. (gd)

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Contact: Simon Kirner simon.kirner@lmu.de 49-892-180-3174 Ludwig-Maximilians-Universitt Mnchen Source:Eurekalert

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