RestrictionDigest: A powerful Perl module for simulating genomic restriction digests|
Wang, Jinpeng; Li, Li; Qi, Haigang; Du, Xuedi & Zhang, Guofan
Background: Reduced-representation sequencing technology iswidely used in genotyping for its economical
and efficient features. A popular way to construct the reduced-representation sequencing libraries is to
digest the genomic DNA with restriction enzymes. A key factor of this method is to determine the
restriction enzyme(s). But there are few computer programs which can evaluate the usability of
restriction enzymes in reduced-representation sequencing. SimRAD is an R package which can simulate
the digestion of DNA sequence by restriction enzymes and return enzyme loci number as well as
fragment number. But for linkage mapping analysis, enzyme loci distribution is also an important factor
to evaluate the enzyme. For phylogenetic studies, comparison of the enzyme performance across multiple
genomes is important. It is strongly needed to develop a simulation tool to implement these functions.
Results: Here, we introduce a Perl module named RestrictionDigest with more functions and improved
performance. It can analyze multiple genomes at one run and generate concise comparison of enzyme
performance across the genomes. It can simulate single-enzyme digestion, double-enzyme digestion and
size selection process and generate comprehensive information of the simulation including enzyme loci
number, fragment number, sequences of the fragments, positions of restriction sites on the genome, the
coverage of digested fragments on different genome regions and detailed fragment length distribution.
Conclusions: RestrictionDigest is an easy-to-use Perl module with flexible parameter settings.With the help
of the information produced by the module, researchers can easily determine the most appropriate
enzymes to construct the reduced-representation libraries to meet their experimental requirements.
Genotyping; Reduced-representation libraries; Reduced-representation sequencing