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

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dc.contributor.author Firth, Andrew E.
dc.contributor.author Patrick, Wayne M.
dc.date.accessioned 2017-11-14T13:24:32Z
dc.date.available 2017-11-14T13:24:32Z
dc.date.issued 2008
dc.identifier.citation 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 en
dc.identifier.volume 36
dc.identifier.issued W2
dc.identifier.startpage 281
dc.identifier.endpage 285
dc.identifier.issn 0305-1048
dc.identifier.uri http://hdl.handle.net/10468/5031
dc.identifier.doi 10.1093/nar/gkn226
dc.description.abstract 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. en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Oxford University Press en
dc.relation.uri https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkn226
dc.rights © 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. en
dc.rights.uri https://creativecommons.org/licenses/by-nc/2.0/uk/
dc.subject Iterative saturation mutagenesis en
dc.subject Directed evolution en
dc.subject Computer program en
dc.subject Enzymes en
dc.subject Strategies en
dc.subject Recombination en
dc.subject Construction en
dc.title GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Andrew Firth, BioSciences Institute, University College Cork, Cork, Ireland. +353-21-490-3000 Email: a.firth@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.description.status Peer reviewed en
dc.identifier.journaltitle Nucleic Acids Research en
dc.internal.IRISemailaddress a.firth@ucc.ie en


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© 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. Except where otherwise noted, this item's license is described as © 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.
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