GeMS: an advanced software package for designing synthetic genes - PubMed (original) (raw)
GeMS: an advanced software package for designing synthetic genes
Sebastian Jayaraj et al. Nucleic Acids Res. 2005.
Abstract
A user-friendly, advanced software package for gene design is described. The software comprises an integrated suite of programs-also provided as stand-alone tools-that automatically performs the following tasks in gene design: restriction site prediction, codon optimization for any expression host, restriction site inclusion and exclusion, separation of long sequences into synthesizable fragments, T(m) and stem-loop determinations, optimal oligonucleotide component design and design verification/error-checking. The output is a complete design report and a list of optimized oligonucleotides to be prepared for subsequent gene synthesis. The user interface accommodates both inexperienced and experienced users. For inexperienced users, explanatory notes are provided such that detailed instructions are not necessary; for experienced users, a streamlined interface is provided without such notes. The software has been extensively tested in the design and successful synthesis of over 400 kb of genes, many of which exceeded 5 kb in length.
Figures
Figure 1
Overview of the synthon design process showing the placement of Type IIs restriction sites and flanking primers. A and B indicate sites of cleavage at synthon edges by Type IIs enzymes to form cohesive ends for seamless ligations.
Figure 2
Sequence of operations during the course of automated gene design; a failure triggers an attempt to redesign the gene with a randomly chosen set of codons. Asterisks indicate steps that are skipped when designing native DNA sequences.
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References
- Withers-Martinez C., Carpenter E.P., Hackett F., Ely B., Sajid M., Grainger M., Blackman M.J. PCR-based gene synthesis as an efficient approach for expression of the A+T-rich malaria genome. Protein Eng. 1999;12:1113–1120. - PubMed
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