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Open Access Software

Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization

Sang-Kyu Jung and Karen McDonald*

Author Affiliations

Department of Chemical Engineering and Materials Science, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA

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BMC Bioinformatics 2011, 12:340  doi:10.1186/1471-2105-12-340

Published: 16 August 2011

Abstract

Background

Direct gene synthesis is becoming more popular owing to decreases in gene synthesis pricing. Compared with using natural genes, gene synthesis provides a good opportunity to optimize gene sequence for specific applications. In order to facilitate gene optimization, we have developed a stand-alone software called Visual Gene Developer.

Results

The software not only provides general functions for gene analysis and optimization along with an interactive user-friendly interface, but also includes unique features such as programming capability, dedicated mRNA secondary structure prediction, artificial neural network modeling, network & multi-threaded computing, and user-accessible programming modules. The software allows a user to analyze and optimize a sequence using main menu functions or specialized module windows. Alternatively, gene optimization can be initiated by designing a gene construct and configuring an optimization strategy. A user can choose several predefined or user-defined algorithms to design a complicated strategy. The software provides expandable functionality as platform software supporting module development using popular script languages such as VBScript and JScript in the software programming environment.

Conclusion

Visual Gene Developer 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. The software is available for free download at http://www.visualgenedeveloper.net webcite.