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Nucleic Acids Research 2005 33(9):3011-3016; doi:10.1093/nar/gki614
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Published online 23 May 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

GeMS: an advanced software package for designing synthetic genes

Sebastian Jayaraj, Ralph Reid and Daniel V. Santi*

KOSAN Biosciences Inc. 3832 Bay Center Place, Hayward, CA 94545, USA

*To whom correspondence should be addressed. Tel: +1 510 731 5204; Fax: +1 510 732 8401; Email: santi{at}kosan.com

Received April 4, 2005. Revised May 5, 2005. Accepted May 5, 2005.

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, Tm 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.


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