DRIVeR: Diversity Resulting from In Vitro Recombination

Version 2006-09-29/02:36:23.

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 generated by random recombination of two near-identical genes differing at only a small number of known nucleotide (or amino acid) positions, we wish to calculate the expected number of distinct sequences in the library. (Typically assuming the mean number of crossovers per sequence m < 0.1 x sequence length N).

Click here for a worked example.

Click here for some caveats.

Input:

Calculate expected number of distinct sequences in a library:

.

.

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This is counting: , or (See note on counting crossovers.)

Positions of variable nucleotides (or amino acids). (Maximum 15 or 20):

(Maximum 20 variable positions.)

(Maximum 15 variable positions.)

How long will it take?

 

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