Gene design software tools | Synthetic biology

Gene design software tools aim to guide the redesign of protein-coding genes using pre-defined features of interest, predominantly targeting improved protein expression, and simplified DNA sequence manipulation. Source text: Gould et al., 2014.

Desktop app
Gene Designer Gene Designer

Gene Designer

Designs sequences de novo without being limited by what nature can provide.…

Designs sequences de novo without being limited by what nature can provide. Gene Designer is a standalone software tool for fast and easy design of synthetic DNA segments. Users can easily add, edit…

TeselaGen TeselaGen

TeselaGen

Gives you the most advanced cloud based solution for combinatorial gene design…

Gives you the most advanced cloud based solution for combinatorial gene design and editing. DNA design & fabrication integrating the best in modern cloning, PCR, direct synthesis, and gene…

Desktop app
Web app
CDSfold CDSfold

CDSfold

An algorithm for designing a protein-coding sequence (CDS) with the most stable…

An algorithm for designing a protein-coding sequence (CDS) with the most stable secondary structure among all possible ones translated into the same protein. The algorithm runs the Zuker algorithm…

Web app
ATGme ATGme

ATGme

Identifies rare and highly rare codons displaying them in the input-sequence as…

Identifies rare and highly rare codons displaying them in the input-sequence as colored codons. ATGme offers three methods of optimization: 1. one-click optimization, 2. bulk optimization, 3. custom…

Codon Usage Database Codon Usage Database

Codon Usage Database

Contains codon usage frequencies for 3,027,973 complete protein coding genes in…

Contains codon usage frequencies for 3,027,973 complete protein coding genes in 35,799 organisms. The use of the database is facilitated by keyword based search analysis and the availability of codon…

Desktop app
Web app
CodonW CodonW

CodonW

Designs to simplify the multivariate analysis (correspondence analysis) of…

Designs to simplify the multivariate analysis (correspondence analysis) of codon and amino acid usage. CodonW also calculates standard indices of codon usage.

Web app
graphical codon usage… graphical codon usage analyser

gcua graphical codon usage analyser

Differences in codon usage preference among organisms lead to a variety of…

Differences in codon usage preference among organisms lead to a variety of problems concerning heterologous gene expression but can be overcome by rational gene design and gene synthesis. The gcua…

Web app
CodonO CodonO

CodonO

A user-friendly tool for codon usage bias analyses across and within genomes in…

A user-friendly tool for codon usage bias analyses across and within genomes in real time. CodonO has three major computational features for codon usage bias analyses: (i) it calculates the codon…

Synthetic Gene… Synthetic Gene Database

SGDB Synthetic Gene Database

A relational database that houses sequences and associated experimental…

A relational database that houses sequences and associated experimental information on synthetic (artificially engineered) genes from all peer-reviewed studies published to date. At present, the…

Web app
Oligonucleotide… Oligonucleotide Architecting

OligArch Oligonucleotide Architecting

Permits synthetic biologists to engineer optimally self-assembling DNA…

Permits synthetic biologists to engineer optimally self-assembling DNA constructs from both six- and eight-letter AEGIS alphabets. This software tool has been used to design oligonucleotides that…

Desktop app
EuGene EuGene

EuGene

A gene optimisation software tool. EuGene focuses on automatically retrieving…

A gene optimisation software tool. EuGene focuses on automatically retrieving information from biological databases and using expert algorithms to redesign genes for heterologous expression. It…

Desktop app
mRNA optimiser mRNA optimiser

mRNA optimiser

Redesigns a gene messenger RNA to optimize its secondary structure, without…

Redesigns a gene messenger RNA to optimize its secondary structure, without affecting the polypeptide sequence. mRNA optimiser can either maximize or minimize the molecule minimum free energy (MFE),…

Desktop app
Ambiguous Nucleotide… Ambiguous Nucleotide Tool

ANT Ambiguous Nucleotide Tool

A desktop application that generates and evaluates degenerate codons.…

A desktop application that generates and evaluates degenerate codons. Degenerate codons are used to represent DNA positions that have multiple possible nucleotide alternatives. This is useful for…

Web app
Codon Optimization… Codon Optimization OnLine

COOL Codon Optimization OnLine

Provides the multi-objective codon optimization functionality to aid systematic…

Provides the multi-objective codon optimization functionality to aid systematic synthetic gene design. COOL supports a simple and flexible interface for customizing various codon optimization…

Web app
GeneDesign GeneDesign

GeneDesign

The manual design of synthetic genes is a tedious and error-prone process-even…

The manual design of synthetic genes is a tedious and error-prone process-even for very short genes-and it becomes completely infeasible when multiple synthetic genes are needed. GeneDesign is a set…

Web app
OPTIMIZER OPTIMIZER

OPTIMIZER

An on-line application that optimizes the codon usage of a gene to increase its…

An on-line application that optimizes the codon usage of a gene to increase its expression level. Three methods of optimization are available: the 'one amino acid-one codon' method, a…

Web app
Synthetic Gene… Synthetic Gene Designer

Synthetic Gene Designer

A web-based tool with the gene optimization functionality including codon usage…

A web-based tool with the gene optimization functionality including codon usage optimization based on CAI score, restriction site elimination, repetitious segment elimination, and oligo generation.…

Desktop app
Visual gene developer Visual gene developer

Visual gene developer

A unique gene design software. Visual Gene Developer provides a user-friendly…

A unique gene design software. Visual Gene Developer provides a user-friendly interface and includes many useful functions such as mRNA secondary structure/binding energy prediction, codon usage/mRNA…

Web app
DNAWorks DNAWorks

DNAWorks

Automates the design of oligonucleotides for gene synthesis by PCR-based…

Automates the design of oligonucleotides for gene synthesis by PCR-based methods. DNAWorks requires simple input information, i.e. amino acid sequence of the target protein and melting temperature…

Web app
Java Codon Adaptation… Java Codon Adaptation Tool

Jcat Java Codon Adaptation Tool

A method for the adaptation of target gene codon usage to most sequenced…

A method for the adaptation of target gene codon usage to most sequenced prokaryotes and selected eukaryotic gene expression hosts was developed to improve heterologous protein production. In…

Desktop app
DNA-Tailor DNA-Tailor

D-Tailor DNA-Tailor

A fully extendable software framework, for property-based design of synthetic…

A fully extendable software framework, for property-based design of synthetic DNA sequences. D-Tailor permits the seamless integration of multiple sequence analysis tools into a generic Monte Carlo…

Web app
Benchling Benchling

Benchling

An ever-expanding app store for designing experiments and analyzing data.…

An ever-expanding app store for designing experiments and analyzing data. Benchling includes the premier suite for molecular biology research: CRISPR guide design, automated Gibson and Golden Gate…

Desktop app
Web app
GeneGenie GeneGenie

GeneGenie

Supports the design and self-assembly of synthetic genes and constructs.…

Supports the design and self-assembly of synthetic genes and constructs. GeneGenie allows for the design of oligonucleotide cohorts encoding the gene sequence optimized for expression in any suitable…

Desktop app
GeMS Deprecated GeMS

GeMS

A user-friendly, advanced software package for the design of synthetic genes.…

A user-friendly, advanced software package for the design of synthetic genes. The software was developed to design synthetic genes to be made by the PCR assembly of short oligos, but it should be…

Desktop app
TmPrime Deprecated TmPrime

TmPrime

A computer program to design oligonucleotide sets for gene assembly by both…

A computer program to design oligonucleotide sets for gene assembly by both ligase chain reaction (LCR) and polymerase chain reaction (PCR). TmPrime offers much flexibility with no constraints on the…

Desktop app
Gene composer Deprecated Gene composer

Gene composer

A database software package which facilitates the information-rich design of…

A database software package which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous…

Web app
UpGene Deprecated UpGene

UpGene

DNA codon optimization is a standard molecular biology strategy to overcome…

DNA codon optimization is a standard molecular biology strategy to overcome poor gene expression. UpGene is a DNA optimization algorithm integrated with a PCR primer design program to redesign…

Web app
DyNAVacS Deprecated DyNAVacS

DyNAVacS

A web-based tool created for rapid and easy design of DNA vaccines. DyNAVacS…

A web-based tool created for rapid and easy design of DNA vaccines. DyNAVacS follows a step-wise design flow, which guides the user through the various sequential steps in the design of the vaccine.…

Web app
Gene2Oligo Gene2Oligo

Gene2Oligo

A web-based tool that divides a long input DNA sequence into a set of adjacent…

A web-based tool that divides a long input DNA sequence into a set of adjacent oligonucleotides representing both DNA strands. The length of the oligonucleotides is dynamically optimized to ensure…

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