In:
Bioinformatics, Oxford University Press (OUP), Vol. 33, No. 11 ( 2017-06-01), p. 1613-1620
Abstract:
Enhancing expression levels of a target protein is an important goal in synthetic biology. A widely used strategy is to integrate multiple copies of genes encoding a target protein into a host organism genome. Integrating highly similar sequences, however, can induce homologous recombination between them, resulting in the ultimate reduction of the number of integrated genes. Results We propose a method for designing multiple protein-coding sequences (i.e. CDSs) that are unlikely to induce homologous recombination, while encoding the same protein. The method, which is based on multi-objective genetic algorithm, is intended to design a set of CDSs whose nucleotide sequences are as different as possible and whose codon usage frequencies are as highly adapted as possible to the host organism. We show that our method not only successfully designs a set of intended CDSs, but also provides insight into the trade-off between nucleotide differences among gene copies and codon usage frequencies. Availability and Implementation Our method, named Tandem Designer, is available as a web-based application at http://tandem.trahed.jp/tandem/. Supplementary information Supplementary data are available at Bioinformatics online.
Type of Medium:
Online Resource
ISSN:
1367-4803
,
1367-4811
DOI:
10.1093/bioinformatics/btx030
Language:
English
Publisher:
Oxford University Press (OUP)
Publication Date:
2017
detail.hit.zdb_id:
1468345-3
SSG:
12
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