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Synthetic biology tools

ApE

OMIC_04795

ApE

A software tool for viewing, editing and analyzing plasmid sequences.

A software tool for viewing, editing and analyzing plasmid sequences.

BioPartsBuilder

OMIC_10634

BioPartsBuilder

A biologist-friendly web tool to design biological parts that are compatible with DNA…

A biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. BioPartsBuilder retrieves biological sequences, enforces compliance with assembly design…

CLONEQC

OMIC_08802

CLONEQC

A lightweight software pipeline available as a free web server and as source code that…

A lightweight software pipeline available as a free web server and as source code that performs quality control on sequenced clones. Input to the server is a list of desired sequences and forward and reverse reads for each clone. The server…

DeviceEditor

OMIC_04782

DeviceEditor

Provides a graphical design environment that mimics the intuitive visual whiteboard…

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…

Geneious

OMIC_00016

Geneious

A powerful and comprehensive suite of molecular biology tools that provides visual…

A powerful and comprehensive suite of molecular biology tools that provides visual sequence alignment and editing, sequence assembly with a clear graphical interface, comprehensive molecular cloning and phylogenetic analysis. First released in 2005,…

Genome Compiler

OMIC_08754

Genome Compiler

Provides the industry with a comprehensive platform for all your synthetic biology needs.…

Provides the industry with a comprehensive platform for all your synthetic biology needs. You will benefit from direct connections to an array of DNA synthesis providers, lab facility services and an extensive suite of advanced bio-informatics tools…

GenoREAD

OMIC_01823

GenoREAD

A web-based application that breaks the sequence verification process into two steps: the…

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…

j5

OMIC_04724

j5

Automates the design of scar-less multipart DNA assembly protocols including SLIC,…

Automates the design of scar-less multipart DNA assembly protocols including SLIC, Gibson, CPEC, and Golden Gate. The key innovations of the j5 design process include cost optimization, leveraging DNA synthesis when cost-effective to do so, the…

Pigeon

OMIC_04783

Pigeon

A web-based tool that translates a textual description of a synthetic biology design into…

A web-based tool that translates a textual description of a synthetic biology design into an image. Pigeon allows programmatic generation of design visualizations, is easy to learn, is easily extensible to new glyphs and notation, and can be…

PromoterCAD

OMIC_08762

PromoterCAD

A web application for designing synthetic promoters with altered transcriptional…

A web application for designing synthetic promoters with altered transcriptional regulation. PromoterCAD is built on the LinkData open platform for data publication and rapid web application development, allowing new data to be easily added, and the…

Pydna

OMIC_08626

Pydna

An extensible, free and open source Python library for simulating basic molecular biology…

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…

QuickGene

OMIC_04726

QuickGene

A molecular biology program for DNA analysis, assembly and cloning. Built by scientists…

A molecular biology program for DNA analysis, assembly and cloning. Built by scientists for scientists, its goal is to be exceedingly user-friendly and intuitive, while making no sacrifices in functionality and incorporating all necessary functions…

R2oDNA Designer

OMIC_04767

R2oDNA Designer

A web application that stochastically generates orthogonal sets of synthetic DNA…

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…

Raven

OMIC_08737

Raven

Uses a sophisticated dynamic programming algorithm to design high-quality DNA assembly…

Uses a sophisticated dynamic programming algorithm to design high-quality DNA assembly plans. Raven produces SBOL compliant images that visualize your assembly plan as well as human readable instructions. Design DNA assembly plans using popular and…

SimVector

OMIC_04725

SimVector

Performs restriction mapping, restriction analysis, plasmid map drawing, gateway, TA and…

Performs restriction mapping, restriction analysis, plasmid map drawing, gateway, TA and restriction cloning.