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OPTIMIZER specifications


Unique identifier OMICS_08710
Interface Web user interface
Restrictions to use None
Input data DNA or Protein sequences
Programming languages PHP
Computer skills Basic
Stability Stable
Maintained Yes

Publications for OPTIMIZER

OPTIMIZER citations


Development of a novel Francisella tularensis Live Vaccine Strain expressing ovalbumin provides insight into antigen specific CD8+ T cell responses

PLoS One
PMCID: 5746256
PMID: 29284034
DOI: 10.1371/journal.pone.0190384

[…] 6xHis tag, stop codon, and flanking XhoI and XbaI sites), the LVS codon frequency table from the Codon Usage DB (http://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=376619) was imported into OPTIMIZER (genomes.urv.es/OPTIMIZER) using the standard setting of “one amino acid–one codon” []. The codon-optimized sequence was submitted for synthesis to Integrated DNA Technologies as a gBlock Ge […]


Predicting synonymous codon usage and optimizing the heterologous gene for expression in E. coli

Sci Rep
PMCID: 5577221
PMID: 28855614
DOI: 10.1038/s41598-017-10546-0

[…] he codon usage pattern of the host strain of the expression system and the codon selection constraints of the target gene–.Many methods, including COOL, Gene Designer, Gene composer, JCat, COStar and OPTIMIZER, have been proposed to design heterologous genes which are expected to be efficiently expressed in the host organism. Based on our knowledge, these methods are prone to select the high-frequ […]


Boosting isoprene production via heterologous expression of the Kudzu isoprene synthase gene (kIspS) into Bacillus spp. cell factory

PMCID: 5548705
PMID: 28791618
DOI: 10.1186/s13568-017-0461-7

[…] ng codon usage database (http://www.kazusa.or.jp/codon/). Then the P. montana (kudzu) isoprene synthase (kIspS) original sequence of GenBank Accession No. AY316691 was optimized using the online tool optimizer (http://genomes.urv.es/OPTIMIZER/). Comparison between the kIspS original sequence, the codon optimized kIspS sequence for B. subtilis and B. licheniformis showed that there are differences […]


In Vivo Indicators of Cytoplasmic, Vacuolar, and Extracellular pH Using pHluorin2 in Candida albicans

PMCID: 5497024
PMID: 28685162
DOI: 10.1128/mSphere.00276-17

[…] F-KpnI and TEF1prR-SalI and cloned between the KpnI and SalI sites of pKE1 to replace the ACT1 promoter. The coding sequence of PHL2 () was optimized for efficient translation in C. albicans with the Optimizer online tool () (; http://genomes.urv.es/OPTIMIZER/), using the combined codon biases of the highly expressed genes RPL29, RPL32, RPL39, ACT1, and ENO1, and synthesized as a gBlock (Integrate […]


CRISPR–Cas9 enabled genetic disruptions for understanding ethanol and ethyl acetate biosynthesis in Kluyveromyces marxianus

Biotechnol Biofuels
PMCID: 5483312
PMID: 28652865
DOI: 10.1186/s13068-017-0854-5

[…] mer P1626/P1530. The Cas9 and sgRNA fragments were inserted into the digested pJSK316-GPD by Gibson Assembly []. For increased editing efficiency, the Cas9 nuclease sequence was codon optimized using Optimizer (http://genomes.urv.es/OPTIMIZER/) and the codon usage table for K. marxianus []. The resulting sequence was then manually altered, as shown in Additional file : Figure S8, to allow for prod […]


Experimental recreation of the evolution of lignin degrading enzymes from the Jurassic to date

Biotechnol Biofuels
PMCID: 5356311
PMID: 28331543
DOI: 10.1186/s13068-017-0744-x

[…] s, together with the two alternative sequences from the CaPo subsets, were synthesized by ATG:biosynthetics (Merzhausen, Germany) after optimizing the codon usage for high expression in E. coli using OPTIMIZER []. […]


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OPTIMIZER institution(s)
Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Faculty of Chemistry, Rovira i Virgili University (URV), c/Marcel·li Domingo, Tarragona, Spain


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