Estimating DNA Library Statistics and Diversity

Statistics of randomized library construction

We have investigated the statistics associated with constructing and sampling large, randomized protein-encoding libraries. Using fairly simple statistics we have written a number of algorithms for estimating the diversity in libraries generated by the most commonly-used randomization methods (see below). These are available through a web interface or by downloading the source code:

Web interface	Programmes and information	Brief Description
GLUE	GLUE	Broadly applicable to any randomization technique where all (DNA) daughter variants are equally likely: oligonucleotide-directed randomization, site-saturation mutagenesis, MAX randomization, synthetic shuffling, etc.
GLUE-IT	-	GLUE-Including Translation: estimate amino acid diversity in libraries with up to 6 variable codons.
CodonCalculator AA-Calculator	- -	Calculate amino acids encoded by a user-specified, partially- or fully-randomized codon. Find optimal XYZ codons to encode selected amino acids.
PEDEL	PEDEL	Programme for Estimating Diversity in Error-prone PCR Libraries.
PEDEL-AA	-	Estimate the number of distinct protein variants encoded by an error-prone PCR library.
DRIVeR	DRIVeR	Diversity Resulting from In Vitro Recombination (i.e. DNA shuffling and StEP PCR).

Mathematical notes for GLUE, PEDEL and DRIVeR: pdf, ps.
Notes on the PEDEL-AA algorithms: html.

References:

Firth A. E., Patrick W. M., 2008, GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries, Nucleic Acids Research, 36, W281-W285. [CodonCalculator, AA-Calculator, GLUE-IT and PEDEL-AA.]
Patrick W. M., Firth A. E., 2005, Strategies and computational tools for improving randomized protein libraries, Biomolecular Engineering, 22, 105-112. [Review article.]
Firth A. E., Patrick W. M., 2005, Statistics of protein library construction, Bioinformatics, 21, 3314-3315. [GLUE, PEDEL and DRIVeR web-server.]
Patrick W. M., Firth A. E., Blackburn J. M., 2003, User-Friendly Algorithms for Estimating Completeness and Diversity in Randomised Protein-Encoding Libraries, Protein Engineering, 16, 451-457. [GLUE, PEDEL and DRIVeR.]

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Notes:

You must agree to the Terms of Usage before using any of this software.
If you use this software for publications, please cite one or more of the above references. Thank you very much.
If you seem to be getting bizarre results, check that none of the limitations on L, N, m etc. have been violated (see the maths notes).
All corrections and notifications of bugs are gratefully received.
Queries or comments to Andrew Firth (aef24cam.ac.uk).
AEF gratefully acknowledges funding from the Foundation for Research, Science and Technology, grant number UOOX0304.