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DNA assembly software tools | Synthetic biology

Molecular biologists routinely clone genetic constructs from DNA segments and formulate plans to assemble them. However, manual assembly planning is complex, error prone and not scalable.

Source text:
(Appleton et al., 2014) Interactive assembly algorithms for molecular cloning. Nat Methods.

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Geneious
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Conducts next generation sequencing (NGS) investigation. Geneious provides visual sequence alignment and editing, sequence assembly, comprehensive molecular cloning and phylogenetic analysis. It increases process efficiency and improves data organization. This tool enables the importation and conversion of a vast range of data types and offers a solution to customize researchers’ algorithms.
GenoREAD
A web-based application that breaks the sequence verification process into two steps: the assembly of sequencing reads and the alignment of the resulting contig with a reference sequence. GenoREAD can determine if a clone matches its reference sequence. Its sophisticated reporting features help identify and troubleshoot problems that arise during the sequence verification process. GenoREAD has been experimentally validated on thousands of gene-sized constructs from an ORFeome project, and on longer sequences including whole plasmids and synthetic chromosomes.
CorGen
Measures long-range correlations in DNA sequences. CorGen is a web application that generate random sequences with the same (or user-specified) correlation and composition parameters. It offers three different types of services: (i) measuring long-range correlations of a given DNA sequence, (ii) generating long-range correlated random sequences with the same statistical parameters as the query sequence and (iii) generating sequences with specific userdefined long-range correlations.
MIDAS / Modular Idempotent DNA Assembly System
Aims to assemble multiple DNA fragments in a single reaction using a standardized assembly design. MIDAS is a program useful for constructing genes from libraries of sequence-verified and contains features allowing genes to be nested between other genes or genetic elements. It permits researchers to create libraries of cloned genetic parts, as libraries of promoters, coding sequences (CDSs) of genes of interest, transcriptional terminators, or fusion tags.
DeviceEditor
Provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions.
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.
PartsGenie
Simplifies the computational design of such synthetic biology parts. PartsGenie allows flexible design of multiple synthetic biology parts through the use of a simple web interface. Designs can be assembled through the arrangement of multiple features, which can be drag-and-dropped from a palette that include ribosome binding sites (RBSs), or coding DNA sequences (CDSs). It offers an integrated UniProt search tool, allowing sequences, NCBI Taxonomy terms and enzyme classification (EC) numbers to be automatically extracted and associated with the CDS, facilitating future traceability.
R2oDNA Designer
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A web application that stochastically generates orthogonal sets of synthetic DNA sequences designed to be biologically neutral. Biologically neutral sequences may be used for directing efficient DNA assembly by overlap-directed methods, as a negative control for functional DNA, as barcodes, or potentially as spacer regions to insulate biological parts from local context. The software creates optimized sequences using a Monte Carlo simulated annealing approach followed by the elimination of sequences homologous to host genomes and commonly used biological parts. An orthogonal set is finally determined by using a network elimination algorithm. Design constraints can be defined using either a web-based graphical user interface (GUI) or uploading a file containing a set of text commands.
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