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Mouse Genome Engineering Using Designer Nucleases

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Published on: April 2, 2014

Gene composer: database software for protein construct design, codon engineering, and gene synthesis.

Don Lorimer¹, Amy Raymond, John Walchli

¹deCODE biostructures, Inc 7869 NE Day Road West, Bainbridge Island, WA 98110, USA. dlorimer@decode.com

BMC Biotechnology

|April 23, 2009

Summary

Gene Composer software enhances protein engineering by streamlining the design of protein constructs and synthetic gene sequences. This tool aids researchers in high-throughput protein structure determination and production.

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Area of Science:

Biochemistry
Molecular Biology
Bioinformatics

Background:

High-throughput protein structure determination requires efficient design of protein constructs and synthetic genes.
Current methods can be cumbersome, necessitating improved bioinformatics tools.

Purpose of the Study:

To develop and present Gene Composer, a database software package for efficient protein construct and synthetic gene design.
To facilitate structure-guided protein engineering and synthetic gene engineering workflows.

Main Methods:

Development of a modular software package with graphical user interfaces.
Implementation of an interactive Alignment Viewer for visualizing sequence and structural data.
Inclusion of Construct Design and Gene Design Modules for protein and gene manipulation.
Automated protein-to-gene back-translation using codon engineering.
Gene-to-oligo algorithm for designing synthetic gene assembly primers.

Main Results:

Gene Composer integrates common bioinformatics steps for protein engineering.
The Alignment Viewer provides multi-contextual visualization of protein properties.
Construct Design Module allows facile modification and virtual cloning of protein constructs.
Gene Design Module automates codon-optimized gene synthesis and primer design.
The system supports PCR-based gene assembly with error correction and PIPE cloning.

Conclusions:

Gene Composer offers comprehensive functionality for designing protein constructs and synthetic genes.
The software facilitates efficient, structure-guided protein engineering.
Designed genes and constructs show potential for improved protein production in structural studies.