RestrictionDigest: A powerful Perl module for simulating genomic restriction digests

Background: Reduced-representation sequencing technology is widely 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 determi...

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Autores principales:	Wang,Jinpeng, Li,Li, Qi,Haigang, Du,Xuedi, Zhang,Guofan
Lenguaje:	English
Publicado:	Pontificia Universidad Católica de Valparaíso 2016
Materias:	Genotyping Reduced-representation libraries Reduced-representation sequencing
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582016000300003
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spelling	oai:scielo:S0717-345820160003000032016-07-06RestrictionDigest: A powerful Perl module for simulating genomic restriction digestsWang,JinpengLi,LiQi,HaigangDu,XuediZhang,Guofan Genotyping Reduced-representation libraries Reduced-representation sequencing Background: Reduced-representation sequencing technology is widely 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.info:eu-repo/semantics/openAccessPontificia Universidad Católica de ValparaísoElectronic Journal of Biotechnology v.19 n.3 20162016-05-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582016000300003en10.1016/j.ejbt.2016.02.003
institution	Scielo Chile
collection	Scielo Chile
language	English
topic	Genotyping Reduced-representation libraries Reduced-representation sequencing
spellingShingle	Genotyping Reduced-representation libraries Reduced-representation sequencing Wang,Jinpeng Li,Li Qi,Haigang Du,Xuedi Zhang,Guofan RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
description	Background: Reduced-representation sequencing technology is widely 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.
author	Wang,Jinpeng Li,Li Qi,Haigang Du,Xuedi Zhang,Guofan
author_facet	Wang,Jinpeng Li,Li Qi,Haigang Du,Xuedi Zhang,Guofan
author_sort	Wang,Jinpeng
title	RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
title_short	RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
title_full	RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
title_fullStr	RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
title_full_unstemmed	RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
title_sort	restrictiondigest: a powerful perl module for simulating genomic restriction digests
publisher	Pontificia Universidad Católica de Valparaíso
publishDate	2016
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582016000300003
work_keys_str_mv	AT wangjinpeng restrictiondigestapowerfulperlmoduleforsimulatinggenomicrestrictiondigests AT lili restrictiondigestapowerfulperlmoduleforsimulatinggenomicrestrictiondigests AT qihaigang restrictiondigestapowerfulperlmoduleforsimulatinggenomicrestrictiondigests AT duxuedi restrictiondigestapowerfulperlmoduleforsimulatinggenomicrestrictiondigests AT zhangguofan restrictiondigestapowerfulperlmoduleforsimulatinggenomicrestrictiondigests
_version_	1718441927401013248

RestrictionDigest: A powerful Perl module for simulating genomic restriction digests

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