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.
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.
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.
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 Analysis Suite. This platform is made for scientists from pharma and biotech companies like government or academic labs. It permits users to share projects with co-worker and to control access to these projects.
Permits to solve the codon optimization problem. GASCO is a web application that calculates the total fitness as a sum of sequence fitness and pattern fitness using a random initial population generated from the standard codon redundancy matrix. It is able to select the codons and engineer the CpG motifs in DNA expression vectors. This tool can be useful in expression cloning, synthetic gene-design and gene-therapy.