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Quantitative analysis of peptide libraries can provide substantial information about molecular interactions that cannot be readily extracted from a qualitative inspection of the results of a phage display experiment. Affinity screening of phage-displayed combinatorial peptide libraries is carried out in order to identify a peptide sequence or sequence motif that binds tightly to a particular molecular target. The result of the experiment is a population of phage particles that represent a subset of the original library that has been enriched for binding to the molecular target. The nucleic acid sequences of the inserts in these phage particles are used to determine the sequences of the displayed peptides whose binding properties presumably led to their selection. In some cases, a sequence motif common to some (or many) of the derived sequences is immediately apparent from a visual inspection of the selected sequences. Frequently, no readily discernable motif can be identified from a visual inspection. This does not necessarily mean that the experiment failed. There are numerous examples in which weak motifs have been identified only after detailed computational analysis of the sequences.

Quantitative analysis can provide insight into at least five aspects of phage-display technology: the quality of a peptide library; the quality or effectiveness of an affinity screen; identification of sequence motifs; identification of binding sites on a protein; and, possibly, identification of proteins that bind to a particular target within an entire genome. This Chapter reviews the existing computational methods available for analyzing populations of peptides and identification of motifs within those populations.

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