Estimating the diversity of peptide populations from limited sequence data.
BACKGROUND
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.
Makowski
Lee
L
Bioscience Division, Argonne National Laboratory, 9700 S. Cass Avenue Argonne, Illinois 60439, USA. lmakowski@anl.gov
Soares
Alexei
A
D000465:Algorithms; D000595:Amino Acid Sequence; D001435:Bacteriophages / Q000235:genetics / Q000378:metabolism; D003062:Codon / Q000235:genetics; D003198:Computer Simulation; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D014644:Genetic Variation / Q000235:genetics* / Q000502:physiology; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D019151:Peptide Library; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*
D003062:Codon; D019151:Peptide Library