Mutanalyst, an online tool for assessing the mutational spectrum of epPCR libraries with poor sampling

BMC Bioinformatics

Software

Matteo Paolo Ferla¹ 

[1] Formerly Department of Biochemistry, University of Otago, Dunedin, New Zealand;Present address: Biosyntia, DTU Centre for Biosustainability, Hørsholm, Denmark;

关键词: Enzyme engineering;    Mutagenesis;    Directed evolution;    Mutational spectrum;    Error-prone mutagenesis;    Standard error;    Confidence;    Small sampling;   

DOI  :  10.1186/s12859-016-0996-7

 received in 2016-02-25, accepted in 2016-03-22,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundAssessing library diversity is an important control step in a directed evolution experiment. To do this, a limited amount of colonies from a test library are sequenced and tested. In the case of an error-prone PCR library, the spectrum of the identified mutations — the proportions of mutations of a specific nucleobase to another— is calculated enabling the user to make more informed predictions on library diversity and coverage. However, the calculations of the mutational spectrum are severely affected by the limited sample sizes.ResultsHere an online program, called Mutanalyst, is presented, which not only automates the calculations, but also estimates errors involved. Specifically, the errors are calculated thanks to the complementarity of DNA, which means that a mutation has a complementary mutation on the other sequence. Additionally, in the case of determining the mean number of mutations per sequence it does so by fitting to a Poisson distribution, which is more robust than calculating the average in light of the small sampling size.ConclusionAs a result of the added measures to keep into account of small sample size the user can better assess whether the library is satisfactory or whether error-prone PCR conditions should be adjusted. The program is available at www.mutanalyst.com.

【 授权许可】

CC BY   
© Ferla. 2016