Pydna: a simulation and documentation tool for DNA assembly strategies using python.
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.
CBMA, Campus de Gualtar, University of Minho, Braga, Portugal. filipaabpereira@gmail.com.
Filipa
F
Pereira
CBMA, Campus de Gualtar, University of Minho, Braga, Portugal. flaviodazevedo@gmail.com.
Flávio
F
Azevedo
CBMA, Campus de Gualtar, University of Minho, Braga, Portugal. ang.mrcarvalho@gmail.com.
Ângela
Â
Carvalho
CBMA, Campus de Gualtar, University of Minho, Braga, Portugal. gabrielafribeiro@gmail.com.
Gabriela F
GF
Ribeiro
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA. markbudde@gmail.com.
Mark W
MW
Budde
CBMA, Campus de Gualtar, University of Minho, Braga, Portugal. bjorn_johansson@bio.uminho.pt.
Björn
B
Johansson
D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D015723:Gene Library; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D058615:Synthetic Biology / Q000379:methods*