GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries
Firth, Andrew E.
Patrick, Wayne M.
Oxford University Press
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.
Iterative saturation mutagenesis , Directed evolution , Computer program , Enzymes , Strategies , Recombination , Construction
Firth, A. E. and Patrick, W. M. (2008) 'GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries', Nucleic Acids Research, 36(W2), pp. 281-285. doi: 10.1093/nar/gkn226
© 2008, the Authors. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/2.0/uk/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.