tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.

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)…
Genome…
Web

Genome Calligrapher

Provides a collection of tunable sequence optimization features. Genome…

Provides a collection of tunable sequence optimization features. Genome Calligrapher automates the DNA sequence optimization of large multipart DNA constructs including multikilobase pair plasmids…

CAIcal
Web
Desktop

CAIcal Codon Adaptation Index cal

Calculates the Codon Adaptation Index (CAI) for a group of sequences using…

Calculates the Codon Adaptation Index (CAI) for a group of sequences using different reference sets. CAIcal is a web-server that includes a complete set of tools related with codon usage adaptation…

CDSfold
Desktop
Web

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…

D-Tailor
Desktop

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…

GeneDesign
Web

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…

CUT
Web

CUT Codon UTilization tool

Allows analysis of all genes or transcripts banked for a species. CUT is based…

Allows analysis of all genes or transcripts banked for a species. CUT is based on a standard “Model View Controller” (MVC). It methodically counts the codon content in gene or transcript…

Codon Usage…
Dataset

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…

OPTIMIZER
Web

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…

DNAWorks
Web

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…

GeneGenie
Desktop
Web

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…

ANT
Desktop

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…

Tandem Designer
Web

Tandem Designer

Yields a set of coding sequences (CDSs) whose nucleotide sequences are as…

Yields a set of coding sequences (CDSs) whose nucleotide sequences are as different as possible and whose codon usage frequencies are as highly adapted as possible to the host organism. Tandem…

SBOLDesigner
Desktop

SBOLDesigner

Allows to fetch and store parts and designs from Synthetic Biology Open…

Allows to fetch and store parts and designs from Synthetic Biology Open Language (SBOL) repositories. SBOLDesigner permits to users to create and manipulate genetic circuits and their sequences by…

CodonO
Web

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…

SGDB
Dataset

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…

mRNA optimiser
Desktop

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),…

Gene2Oligo
Web

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…

Jcat
Web

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…

CodonExplorer
Web

CodonExplorer

Allows rapid testing of hypotheses about codon usage in sequenced genes and…

Allows rapid testing of hypotheses about codon usage in sequenced genes and genomes. CodonExplorer can reveal patterns associated with gene expression changes, mutational biases and horizontal gene…

COOL
Web

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…

ATGme
Web

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…

EuGene
Desktop

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…

OligArch
Web

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…

PromCal
Desktop

PromCal

Allows evaluation of experimental data. PromCal is a web tool developed to…

Allows evaluation of experimental data. PromCal is a web tool developed to provide a tool for calculation of relative promoter strengths from experimental data. The software can be applicable in…

RCDI/eRCDI
Web
Desktop

RCDI/eRCDI Relative Codon Deoptimization Index / Expected RDCI

Performs calculation of the Relative Codon Deoptimization Index (RCDI) and a…

Performs calculation of the Relative Codon Deoptimization Index (RCDI) and a new expected value for the RCDI (eRCDI). RCDI/eRCDI is a program available both as one of and the tools of the CAIcal…

gcua
Web

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…

Gene Designer
Desktop

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…

Visual gene…
Desktop

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…

codcmp
Desktop

codcmp

Reads two codon usage table files and writes to file the differences in codon…

Reads two codon usage table files and writes to file the differences in codon usage fractions between the two tables. codcmp is an Emboss tool. The usage fraction of a codon is its proportion (0 to…

cutgextract
Desktop

cutgextract

Extract codon usage tables from CUTG database. cutgextract looks in the…

Extract codon usage tables from CUTG database. cutgextract looks in the specified directory and opens all the files with the extension '.codon'. Given the name of a directory containing the…

TeselaGen
Desktop

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…

CodonW
Desktop
Web

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.

Synthetic Gene…
Web

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.…

Benchling
Web

Benchling

Allows scientists to design, share, and record experiments or tests. The…

Allows scientists to design, share, and record experiments or tests. The Benchling platform contains a Biological Registration System, an Electronic Lab Notebook, and Molecular Biology Design and…

GeMS
Desktop

GeMS Gene Morphing System

Developed to design of synthetic genes to be made by polymerase chain reaction…

Developed to design of synthetic genes to be made by polymerase chain reaction (PCR) assembly of short oligos. GeMS is a software which contains most components found in other gene synthesis as well…

TmPrime
Desktop

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…

DyNAVacS
Web

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.…

Gene composer
Desktop

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…

The…
Dataset

The gene-specific codon counting database

Compiles and analyzes codon combinations in all budding yeast genes. The…

Compiles and analyzes codon combinations in all budding yeast genes. The gene-specific codon counting database provides a method for analyzing codon runs in both genes and genomes. The database…

UpGene
Web

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…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.