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Nucleic Acids Research Advance Access published online on April 28, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn226
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries

Andrew E. Firth1 and Wayne M. Patrick2,*

1BioSciences Institute, University College Cork, Cork, Ireland and 2Institute of Molecular Biosciences, Massey University, Auckland 0745, New Zealand

*To whom correspondence should be addressed. Tel: +64 9 414 0800, ext. 9694; Fax: +64 9 441 8142; Email: w.patrick{at}massey.ac.nz

Received January 24, 2008. Revised April 7, 2008. Accepted April 10, 2008.

There are many methods for introducing random mutations into nucleic acid sequences. Previously, we described a suite of programmes for estimating the completeness and diversity of randomized DNA libraries generated by a number of these protocols. Our programmes suggested some empirical guidelines for library design; however, no information was provided regarding library diversity at the protein (rather than DNA) level. We have now updated our web server, enabling analysis of translated libraries constructed by site-saturation mutagenesis and error-prone PCR (epPCR). We introduce GLUE-Including Translation (GLUE-IT), which finds the expected amino acid completeness of libraries in which up to six codons have been independently varied (according to any user-specified randomization scheme). We provide two tools for assisting with experimental design: CodonCalculator, for assessing amino acids corresponding to given randomized codons; and AA-Calculator, for finding degenerate codons that encode user-specified sets of amino acids. We also present PEDEL-AA, which calculates amino acid statistics for libraries generated by epPCR. Input includes the parent sequence, overall mutation rate, library size, indel rates and a nucleotide mutation matrix. Output includes amino acid completeness and diversity statistics, and the number and length distribution of sequences truncated by premature termination codons. The web interfaces are available at http://guinevere.otago.ac.nz/stats.html.


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