[Microbiology] OPTIMIZER: a web server for optimizing the codon usage of DNAsequences.

ppuigbo from urv.cat via microbio%40net.bio.net (by ppuigbo from urv.cat)
Wed May 9 10:39:54 EST 2007

I wish to introduce the OPTIMIZER web-server that optimizes the codon us=
age of a gene to increase its expression level=2E This web-server is foc=
used on the heterologous=2C or even homologous=2C gene expression in bac=
terial hosts=2E Two indices=2C CAI and ENc (effective number of codons)=2C=
 are used to measure the optimization process=2E

Three methods of optimization are available=3A =


- The =27one amino acid - one codon=27 method=2E
- A guided random method based on a Monte Carlo algorithm=2E
-The =91customized one amino acid - one codon=92 designed to maximize th=
e optimization with the fewest changes in the query sequence=2E =


One of the main features of OPTIMIZER is that it makes it possible to op=
timize a DNA sequence using the following pre-computed tables from more =
than 150 prokaryotic species under strong translational selection=3A

- Codon usage from a Predicted Group of Highly Expressed Genes=2E
- Codon usage from the Group of Ribosomal Protein Genes=2E
- tRNA Gene Copy Numbers (tGCN)=2E

Additionally=2C codon usage tables from the Codon Usage database (CUTG) =
can also be used=2E

OPTIMIZER is accessible free of charge at http=3A//genomes=2Eurv=2Ees/OP=
 For more details see the article Puigbo et al=2E 2007 Nucleic Acids Res=
earch=2C doi=3A10=2E1093/nar/gkm219 =2E

Pere Puigb=F2 Avalos=2C PhD Student
Evolutionary Genomics Group=2C
Biochemistry and Biotechnology Department=2C
Rovira i Virgily University=2E
C/Marcel=B7l=ED domingo s/n=2E 43007=2E Campus Sescelades=2E Tarragona=2E=

Phone=3A 0034=2E977=2E55=2E84=2E86
Web Page=3A http=3A//genomes=2Eurv=2Ecat
E-mail=3A ppuigbo=40urv=2Ecat

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