ArticleBMC bioinformatics2015
Pydna: a simulation and documentation tool for DNA assembly strategies using python.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 38 citations in OpenAlex.
- A guide to Direct Pathway Cloning (DiPaC) for natural product discovery.Essays in biochemistry · 2026Review
- PoolParty: streamlined design of DNA sequence libraries in Python.bioRxiv : the preprint server for biology · 2026Article
- Assessing PARP trapping dynamics in ovarian cancer using a CRISPR-engineered FRET biosensor.Cell reports methods · 2026Article
- SEGUID v2: Extending SEGUID checksums for circular, linear, single- and double-stranded biological sequences.PloS one · 2026Article
- Metabolic engineering and late-stage functionalization expand the chemical space of the antimalarial premarineosin A.Communications chemistry · 2025Article
- StreptoCAD: An Open-Source Software Toolbox Automating Genome Engineering Workflows in Streptomycetes.ACS synthetic biology · 2025Article
- Data-driven synthetic microbes for sustainable future.NPJ systems biology and applications · 2025Review
- Optimized production of concanamycins using a rational metabolic engineering strategy.Metabolic engineering · 2025Article
- SequenceCraft: machine learning-based resource for exploratory analysis of RNA-cleaving deoxyribozymes.BMC bioinformatics · 2025Article
- teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering.PLoS computational biology · 2024Article
- FBPP: software to design PCR primers and probes for nucleic acid base detection of foodborne pathogens.Scientific reports · 2024Article
- Article
- Optimization of a hybrid bacterial/Metabolic engineering communications · 2023Article
- ASVmaker: A New Tool to Improve Taxonomic Identifications for Amplicon Sequencing Data.Plants (Basel, Switzerland) · 2023Article
- Article
- A framework to efficiently describe and share reproducible DNA materials and construction protocols.Nature communications · 2022Article
- Expression of Yarrowia lipolytica acetyl-CoA carboxylase in Saccharomyces cerevisiae and its effect on in-vivo accumulation of Malonyl-CoA.Computational and structural biotechnology journal · 2022Article
- BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models.Nucleic acids research · 2021Article
- 2-kupl: mapping-free variant detection from DNA-seq data of matched samples.BMC bioinformatics · 2021Article
- Deep diversification of an AAV capsid protein by machine learning.Nature biotechnology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRecent 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.
resultsWe 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.
conclusionsPydna 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.