Please use this identifier to cite or link to this item: http://hdl.handle.net/1822/51148

TitlePydna: a simulation and documentation tool for DNA assembly strategies using python
Author(s)Pereira, Filipa Alexandra Barroso
Azevedo, Flavio
Carvalho, Angela
Ribeiro, Gabriela F.
Budde, Mark W.
Johansson, Björn
KeywordsNext generation cloning
Cloning simulation
Bioinformatics
Homologous recombination
Issue date2015
PublisherBioMed Central (BMC)
JournalBMC Bioinformatics
Abstract(s)Background: Recent advances in synthetic biology have provided tools to efficiently construct complex DNA molecules which are an important part of many molecular biology and biotechnology projects. The planning of such constructs has traditionally been done manually using a DNA sequence editor which becomes error-prone as scale and complexity of the construction increase. A human-readable formal description of cloning and assembly strategies, which also allows for automatic computer simulation and verification, would therefore be a valuable tool.Results: We have developed pydna, an extensible, free and open source Python library for simulating basic molecular biology DNA unit operations such as restriction digestion, ligation, PCR, primer design, Gibson assembly and homologous recombination. A cloning strategy expressed as a pydna script provides a description that is complete, unambiguous and stable. Execution of the script automatically yields the sequence of the final molecule(s) and that of any intermediate constructs. Pydna has been designed to be understandable for biologists with limited programming skills by providing interfaces that are semantically similar to the description of molecular biology unit operations found in literature.Conclusions: Pydna simplifies both the planning and sharing of cloning strategies and is especially useful for complex or combinatorial DNA molecule construction. An important difference compared to existing tools with similar goals is the use of Python instead of a specifically constructed language, providing a simulation environment that is more flexible and extensible by the user.
TypeArticle
URIhttp://hdl.handle.net/1822/51148
DOI10.1186/s12859-015-0544-x
ISSN1471-2105
Peer-Reviewedyes
AccessOpen access
Appears in Collections:DBio - Artigos/Papers

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