As a growing number of companies jostle for position in the emerging market for gene-synthesis services, some are turning to software as a way to differentiate themselves from their competitors.
This week, MWG Biotech of Ebersberg, Germany, announced that it has developed a new software program for “optimizing” synthetic genes. The software, called GENEius and developed in collaboration with partner Eurofins Medigenomix, is primarily for internal use as part of MWG’s gene-synthesis service.
A version with limited features, called “GENEius light” is available here for prospective customers to test drive, according to Tobias Wagner, director of genomic services sales at MWG.
Stefan Blickling, head of European sales at MWG, said in a statement that the software is expected to “strengthen our position as the high-quality provider of synthetic genes.”
Wagner said that a key feature of the software is its ability to automatically optimize codon usage for gene synthesis.
Synthetic genes are primarily used for protein expression, Wagner said, and this process can be compromised by differences in codon usage between organisms.
“If you’re introducing, for example, a human gene into E. coli you can get difficulty in expression and this is mostly based on different codon usages for the organisms,” he said.
For example, the codons AGG and AGA used to code arginine are used with a frequency of 21 percent in humans, but only with a frequency of between 2 and 4 percent in E. coli, respectively.
“Thus, if a gene from human origin is inserted into an E. coli expression system, the tRNA’s of the codons AGG and AGA will be used up very quickly, yielding a very low level of expression,” the company said in a statement.
“With our software we are able to adapt the sequence, for instance, from human to the codon usage of E. coli,” he said, noting that the software can automatically adapt the sequence to the codon usage preferred by any given organism that will express the protein.
“If you’re introducing, for example, a human gene into E. coli you can get difficulty in expression and this is mostly based on different codon usages for the organisms.”
GENEius adjusts the coding sequence for the codon usage of the destination organism in several steps, resulting in “a codon frequency that is nearly identical to the natural conditions,” the company said.
The company said that the software also allows its internal researchers to avoid direct and inverted repeats and hairpins and to ensure even distribution of GC content and incorporation of “good motifs.”
The software could give the firm an edge against competitors like GeneArt, Sloning, Blue Heron Technologies, and a host of other firms that provide gene-synthesis services.
Wagner said that most of these firms have developed their own internal software packages for gene design, and that the field is not yet to the point where off-the-shelf software is widely available for this purpose.
There are several open-source packages available for gene design, however. The biological sciences department at the University of Maryland, Baltimore County, has compiled a list of 35 such programs that is available here.
Wagner said that the software developed by gene synthesis firms tends to be “more sophisticated” than these tools, however, and that GENEius is “much more efficient and highly sophisticated” than that of its competitors.