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.
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.
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.
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.
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.
Enables researchers to create custom target enrichment library designs, microarray designs, and fluorescence in-situ hybridization (FISH) designs. SureDesign is an Agilent web application that permits users to enter target genes or genomic coordinates, define the regions of interest within those targets and define a few probe selection parameters. These information are then used to select probes or oligos to analyze the desired target regions.