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Bioinformatics Vol. 19 no. 4 2003
Pages 483-489
© 2003 Oxford University Press

Estimating the diversity of peptide populations from limited sequence data

Lee Makowski 1,* and Alexei Soares 2

1 Bioscience Division, Argonne National Laboratory, 9700 S. Cass Avenue Argonne, Illinois 60439, USA
2 Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA

Received on July 5, 2002 ; revised on September 20, 2002 ; accepted on September 28, 2002

Motivation: Combinatorial libraries of peptides such as those displayed on the surface of a bacteriophage particle have become widely used tools for characterizing protein–protein and protein–small molecule interactions. The quality of a library frequently depends on its completeness, or diversity—the proportion of possible sequences actually present in the library. The diversity of these libraries is frequently quoted on the basis of phage titers that provide little information about their completeness.

Results: Here, an analytical expression for diversity is introduced and a method for estimating the diversity of a peptide library from the sequences of a limited number of the members of the library is demonstrated. The diversities of a number of computationally constructed and actual peptide libraries are estimated using this method.

Contact: lmakowski{at}anl.gov

* To whom correspondence should be addressed.


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