Statistics of protein library construction

We have investigated the statistics associated with constructing and sampling large protein-encoding libraries. Using fairly simple statistics we have written algorithms for estimating the diversity in libraries generated by the most commonly used protocols, including error-prone PCR, DNA shuffling,...

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Bibliographic Details
Published in:Bioinformatics 2005-08, Vol.21 (15), p.3314-3315
Main Authors: Firth, Andrew E., Patrick, Wayne M.
Format: Article
Language:English
Subjects:
Algorithms
Biological and medical sciences
DNA Mutational Analysis - methods
Evolution, Molecular
Fundamental and applied biological sciences. Psychology
General aspects
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Models, Chemical
Models, Genetic
Models, Statistical
Peptide Library
Polymerase Chain Reaction - methods
Sequence Analysis, DNA - methods
Sequence Analysis, Protein - methods
Software
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Summary:We have investigated the statistics associated with constructing and sampling large protein-encoding libraries. Using fairly simple statistics we have written algorithms for estimating the diversity in libraries generated by the most commonly used protocols, including error-prone PCR, DNA shuffling, StEP PCR, oligonucleotide-directed randomization, MAX randomization, synthetic shuffling, DHR, ADO and SISDC. Availability: Web interface and C++ source code available at http://guinevere.otago.ac.nz/stats.html Contact: aef@sanger.otago.ac.nz Supplementary information: Complete mathematical notes, model assumptions and justification, users' guide and worked examples at above website.
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/bti516