Skip Navigation



Bioinformatics Advance Access published online on June 2, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti516
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/15/3314    most recent
bti516v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Firth, A. E.
Right arrow Articles by Patrick, W. M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Firth, A. E.
Right arrow Articles by Patrick, W. M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received April 14, 2005
Revised May 21, 2005
Accepted May 23, 2005

Applications note

Statistics of protein library construction

Andrew E. Firth 1* and Wayne M. Patrick 2

1 Department of Biochemistry, University of Otago, PO Box 56, Dunedin, New Zealand
2 Center for Fundamental and Applied Molecular Evolution, Emory University, Atlanta, Georgia 30322, USA

* To whom correspondence should be addressed.
Andrew E. Firth, E-mail: aef{at}sanger.otago.ac.nz


  Abstract

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.

Supplementary information: Complete mathematical notes, model assumptions and justification, users' guide, and worked examples at above web site.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Proc. Natl. Acad. Sci. USAHome page
I. C. Tanrikulu, E. Schmitt, Y. Mechulam, W. A. Goddard III, and D. A. Tirrell
Discovery of Escherichia coli methionyl-tRNA synthetase mutants for efficient labeling of proteins with azidonorleucine in vivo
PNAS, September 8, 2009; 106(36): 15285 - 15290.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. E. Firth and W. M. Patrick
GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W281 - W285.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
W. M. Patrick, E. M. Quandt, D. B. Swartzlander, and I. Matsumura
Multicopy Suppression Underpins Metabolic Evolvability
Mol. Biol. Evol., December 1, 2007; 24(12): 2716 - 2722.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
K. U. Walter, K. Vamvaca, and D. Hilvert
An Active Enzyme Constructed from a 9-Amino Acid Alphabet
J. Biol. Chem., November 11, 2005; 280(45): 37742 - 37746.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.