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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…
Raven
Desktop
Web

Raven

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

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…

Genome…
Web

Genome Partitioner

Permits multi-level partitioning of large-scale DNA constructs for synthetic…

Permits multi-level partitioning of large-scale DNA constructs for synthetic biology applications. Genome Partitioner is a web-tool that provides a detailed online documentation including explanation…

BioPartsBuilder
Desktop

BioPartsBuilder

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

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…

GenoREAD
Web

GenoREAD

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

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…

PromoterCAD
Web

PromoterCAD

A web application for designing synthetic promoters with altered…

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…

PartsGenie
Web

PartsGenie

Simplifies the computational design of such synthetic biology parts. 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…

R2oDNA Designer
Desktop
Web

R2oDNA Designer

A web application that stochastically generates orthogonal sets of synthetic…

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…

Pydna
Desktop

Pydna

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

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…

Pigeon
Web

Pigeon

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

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…

j5
Web

j5

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

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…

G T A T C G C T A
Geneious
Desktop

Geneious

Proposes a powerful and comprehensive suite of next generation sequencing (NGS)…

Proposes a powerful and comprehensive suite of next generation sequencing (NGS) analysis tools. Through an intuitive and user-friendly interface, Geneious provides visual sequence alignment and…

DeviceEditor
Web

DeviceEditor

Provides a graphical design environment that mimics the intuitive visual…

Provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual…

Collagene
Desktop

Collagene

Supports and allows reutilization of contemporary cloning methods. Collagene…

Supports and allows reutilization of contemporary cloning methods. Collagene offers advanced functions for the visualization of the results.

G T A T C G C T A
WebDSV
Web

WebDSV

Allows users to work on DNA sequences. WebDSV assists in creation, edition and…

Allows users to work on DNA sequences. WebDSV assists in creation, edition and analysis of DNA sequences. This tool enables visualization of sequences and permits user to mark them. It generates…

Plasmidomics
Desktop

Plasmidomics

Allows user to draw vector and plasmid maps.

Allows user to draw vector and plasmid maps.

Genome Compiler
Desktop

Genome Compiler

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

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…

ApE
Desktop

ApE A plasmid Editor

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

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

QuickGene
Desktop

QuickGene

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

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…

SimVector
Desktop

SimVector

Performs restriction mapping, restriction analysis, plasmid map drawing,…

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

CLONEQC
Desktop
Web

CLONEQC

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

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…

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