[Computational-biology] OPTIMIZER: a web server for optimizing the codon usage of DNAsequences.

ppuigbo from urv.cat via comp-bio%40net.bio.net (by ppuigbo from urv.cat)
Sun May 13 04:03:13 EST 2007


 I wish to introduce the OPTIMIZER web-server that optimizes the codon u=
sage of a gene to increase its expression level=2E This web-server is fo=
cused on the heterologous=2C or even homologous=2C gene expression in ba=
cterial 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 max=
imize the optimization with the fewest changes in the query sequence=2E =

 One of the main features of OPTIMIZER is that it makes it possible to o=
ptimize 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/O=
PTIMIZER =2E
For more details see the article Puigbo et al=2E 2007 Nucleic Acids Rese=
arch=2C doi=3A10=2E1093/nar/gkm219 =2E

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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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