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

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References in zbMATH (referenced in 3 articles )

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  1. Nov, Yuval; Segev, Danny: Optimal codon randomization via mathematical programming (2013)
  2. Kong, Yong: Calculating complexity of large randomized libraries (2009)
  3. Firth, Andrew E.; Patrick, Wayne M.: GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries (2008) ioport