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DNAWorks
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.
OPTIMIZER
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.
Jcat / Java Codon Adaptation Tool
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.
GeneGenie
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.
CDSfold
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.
COOL / Codon Optimization OnLine
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.
Tandem Designer
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.
ANT / Ambiguous Nucleotide Tool
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 protein engineering and directed evolution, where primers specified with degenerate codons are used as a basis for generating libraries of protein sequences. ANT is intuitive and can be used in a graphical user interface or by interacting with the code through a defined application programming interface. ANT comes with full support for nonstandard, user-defined, or expanded genetic codes (translation tables), which is important because synthetic biology is being applied to an ever widening range of natural and engineered organisms.
CAIcal / Codon Adaptation Index cal
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 as the representation of the CAI along a sequence or multi alignment and the estimation of an expected CAI value (eCAI). A graphical local user interface can also be downloaded and allows the calculation of the CAI and eCAI of hundreds or thousands of sequences on a whole-genome scale easily.
Visual gene developer
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 optimization, GC content/Nc (effective number of codons)/CAI calculation, sequence comparison, repeated sequence search, multiple query sequence search, and silent removal of undesirable sequences. It is useful for both researchers who want to quickly analyze and optimize genes, and those who are interested in developing and testing new algorithms in bioinformatics.
RCDI/eRCDI / Relative Codon Deoptimization Index / Expected RDCI
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 server and for local use. The software can be useful for genome analysis and for allowing, in experimental virology, efficient gene design for heterologous protein expression. It can also assist in establishing and understanding host-virus phylogenetic relationships and in inferring the potential host range of a virus and its replication strategy.
SyGS / Synthetic biology Gene Standardizer
Makes silent mutations at every BioBrick, BglBrick, MoClo, and GoldenBraid restriction site for any given protein coding sequence. SyGS automates the standardization of gene sequences to have the broadest compatibility with current synthetic biology cloning strategies. It is able to remove all targeted sites without any necessary amino acid substitutions. This tool offers an interface that allows users to enter a gene name for either Escherichia coli or Bacillus subtilis, or paste a sequence.
pDRAW
Provides a wide range of features for handle DNA data. pDRAW is a free standalone software that authorizes to clone a sequence, including large files, and automatically perform its corresponding restriction enzyme sites or open reading frames. The application also allows users to edit sequences in various ways as well as determine optimal polymerase chain reaction (PCR) annealing temperature. Moreover, it permits to create and export several graphical plots including virtual agarose gel plots.
cutgextract
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 CUTG database, cutgextract will calculate codon usage tables for individual species (e.g. EHomo_sapiens.cut) and place them in the CODONS subdirectory of the EMBOSS data directory. This is an all-or-nothing extraction; it will create many files and take several minutes. The usage tables are calculated from the sum of codons over all sequences for each organism.
codcmp
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 1) of the total number of the codons in the sequences used to construct the usage table. For each codon that is used in both tables, it takes the difference between the usage fractions in the two tables. The sum of the differences and the sum of the differences squared are reported in the output file. It also counts the number of the 64 possible codons which are unused (i.e. has a usage fraction of 0) in either one or the other or both of the codon usage tables, and writes this to the output file.
TmPrime
Obsolete
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 gene and oligonucleotide lengths. The program divides the long input DNA sequence based on the input desired melting temperature, and dynamically optimizes the length of oligonucleotides to achieve homologous melting temperatures. The output reports the melting temperatures, oligonucleotide sequences and potential formation of secondary structures.
GeMS / Gene Morphing System
Obsolete
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 as certain unique features such as automatic spacing or manual placement of unique or redundant restriction sites along the gene sequence. This tool allows creation of hybrid codon preference tables for optimizing gene expression in two or more organisms and separation of long coding sequences into smaller fragments or synthons to be synthesized.
CodonExplorer
Obsolete
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 transfer (HGT). It allows convenient discovery of genes by genome, function or orthology and visualization of the composition of these genes. This tool employs Monte Carlo techniques for testing the statistical significance of differences in codon usage or nucleotide sequence composition.
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SGDB / Synthetic Gene Database
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 database comprises information from more than 200 published experiments. SGDB not only provides reference material to guide experimentalists in designing new genes that improve protein expression, but also offers a dataset for analysis by bioinformaticians who seek to test ideas regarding the underlying factors that influence gene expression.
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