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PEDS Advance Access originally published online on October 20, 2005
Protein Engineering Design and Selection 2005 18(12):559-561; doi:10.1093/protein/gzi061
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org

COMMUNICATION

Automated design of degenerate codon libraries

Marco A. Mena and Patrick S. Daugherty1

Department of Chemical Engineering, University of California, Santa Barbara Santa Barbara, CA 93106-9510, USA

1 To whom correspondence should be addressed. E-mail: psd{at}engineering.ucsb.edu

Degenerate codon libraries are frequently used in protein engineering and evolution studies but are often limited to targeting a small number of positions to adequately limit the search space. To mitigate this, codon degeneracy can be limited using heuristics or previous knowledge of the targeted positions. To automate design of libraries given a set of amino acid sequences, an algorithm (LibDesign) was developed that generates a set of possible degenerate codon libraries, their resulting size, and their score relative to a user-defined scoring function. A gene library of a specified size can then be constructed that is representative of the given amino acid distribution or that includes specific sequences or combinations thereof. LibDesign provides a new tool for automated design of high-quality protein libraries that more effectively harness existing sequence–structure information derived from multiple sequence alignment or computational protein design data.

Keywords: algorithm/codon/degenerate/design/library

Received March 2, 2005; revised June 21, 2005; accepted August 13, 2005.

Edited by Andreas Plueckthun


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