PEDEL: Programme for Estimating Diversity in Error-prone PCR Libraries

Note:This page is a work in progress; currently only the Poisson distribution option works.

Version 2008-01-20/06:37:22.

The programme is introduced in Wayne M. Patrick, Andrew E. Firth, Jonathan M. Blackburn, 2003, User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries, Protein Engineering, 16, 451-457, and Andrew E. Firth, Wayne M. Patrick, 2005, Statistics of protein library construction, Bioinformatics, 21, 3314-3315.

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Problem: Given a library of L sequences, comprising variants of a sequence of N nucleotides, into which random point mutations have been introduced, we wish to calculate the expected number of distinct sequences in the library. (Typically assuming L > 10, N > 5, and the mean number of mutations per sequence m < 0.1 x N).

Click here for a worked example.

Click here for some caveats.

See also:

• Plot and tabulate more detailed statistics (e.g. the expected number of sequences, expected number of distinct sequences, and number of possible sequences, with exactly 1, 2, 3, ... mutations).
• Calculate and plot the expected number of distinct sequences in a library for a range of mutation rates.
• Calculate and plot the expected number of distinct sequences in a library for a range of library sizes.
• Calculate and plot the expected number of distinct sequences in a library for a range of sequence lengths.