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.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
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 of web applications that provides public access to a nucleotide manipulation pipeline for synthetic biology.
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 guided random method based on a Monte Carlo algorithm, and a method designed to maximize the optimization with the fewest changes in the query sequence. One of the main features of OPTIMIZER is that it makes it possible to optimize a DNA sequence using pre-computed codon usage tables from a predicted group of highly expressed genes from more than 150 prokaryotic species under strong translational selection.
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 (needed for the gene assembly) of synthetic oligonucleotides. The program outputs a series of oligonucleotide sequences with codons optimized for expression in an organism of choice. Those oligonucleotides are characterized by highly homogeneous melting temperatures and a minimized tendency for hairpin formation.
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 contrast to existing tools, JCat does not require the manual definition of highly expressed genes and is, therefore, a very rapid and easy method. Further options of JCat for codon adaptation include the avoidance of unwanted cleavage sites for restriction enzymes and Rho-independent transcription terminators. The output of JCat is both graphically and as Codon Adaptation Index (CAI) values given for the pasted sequence and the newly adapted sequence. Additionally, a list of genes in FASTA-format can be uploaded to calculate CAI values.
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 both the specificity and the uniform melting temperatures necessary for in vitro gene synthesis.
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 usage bias for one or more genomes; (ii) it compares and visualizes the correlation between codon usage bias and GC compositions; (iii) it performs statistical analyses for codon usage bias within and across genomes.
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 host through an intuitive, easy-to-use web interface. The tool ensures consistent oligomer overlapping melting temperatures, minimizes the likelihood of misannealing, optimizes codon usage for expression in a selected host, allows for specification of forward and reverse cloning sequences (for downstream ligation) and also provides support for mutagenesis or directed evolution studies.
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), thus resulting in decreased or increased secondary structure strength. Evaluations of the secondary structure are made using a correlated stem-loop prediction algorithm that examines the nucleotide sequence for simple stem-loops.
A web-based tool for rapid optimization of degenerate codons. SwiftLib optimizes a degenerate codon library to cover the desired set of amino acids at several positions while staying within a diversity limit for the library. It is a fast way to generate small libraries.
Calculates covariance scores for constrained regions of background conservation. McBASC can be utilized as a covarying or highly conserved filter. This software gives an equally high score to conserved or covarying alignments and allows, without a reduction in score, substitution of conserved pairs of residues for covarying ones.
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 graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering.
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 simulation that evolves sequences toward any combination of rationally defined properties.
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 under the constraint of a given amino acid sequence. The time and space complexity is O(L3) and O(L2), respectively, where L is the length of the CDS to be designed. Although our algorithm is slower than the original Zuker algorithm, it could design a relatively long (2.7-kb) CDS in approximately 1 h. The algorithm is useful for investigating the effect of the secondary structure of a CDS as well as utilizing features of the secondary structure to control protein expression levels.
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 allows opening and parsing genome files, analysing gene and protein sequences, and redesigning them according to several biological factors such as codon usage, codon context, GC content, hidden stop codons, repeated codons or nucleotides, harmonisation, deleterious sequences, etc.
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 parameters such as codon adaptation index, individual codon usage and codon pairing. In addition, users can visualize and compare the optimal synthetic sequences with respect to various fitness measures. User-defined DNA sequences can also be compared against the COOL optimized sequences to show the extent by which the user's sequences can be further improved.
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 Designer is a method for designing a set of CDSs that are not only unlikely to induce homologous recombination when integrated into a genome, but also have highly adapted codon usage frequencies. This platform optimizes sequences to increase nucleotide differences among CDSs that encode the same target protein.
Provides a collection of tunable sequence optimization features. Genome Calligrapher automates the DNA sequence optimization of large multipart DNA constructs including multikilobase pair plasmids and entire synthetic genomes. User have to specify a GenBank sequence for server upload to begin the DNA synthesis optimization process. The Genome Calligrapher algorithm uses built-in rules for removal of homopolymeric sequences and di- and tri-nucleotide repeats.
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 using the SBOL data standard. It is able to import and export data about parts and designs in SBOL 1, GenBank, and FASTA data format. The tool can make connections with circuit genetic design automation (GDA) tools.