CAIcal SERVER

Puigbo et al. (2008) BMC Bioinformatics,9:65.
     Puigbo et al. (2010) BMC Reasearch Notes,3:87.


The CAIcal server is freely available at http://genomes.urv.es/CAIcal. This server performs several computations in relation to codon usage and the codon adaptation of DNA or RNA sequences to host organisms.

HOW TO CITE: Puigbo P, Bravo IG and Garcia-Vallve S. (2008) CAIcal: a combined set of tools to assess codon usage adaptation. Biology Direct, 3:38.



Calculation of parameters:

Use this option to calculate nucleotide composition, codon usage, codon usage per thousand and/or Relative Synonymous Codon Usage (RSCU) from DNA sequences.



Click here to see an example


DNA or RNA sequences:

Use this option to calculate (a) Codon Adaptation Index (CAI) from DNA sequences or (b) expected CAI determined by randomly generating sequences.

[CAI calculation]

[Calc expected CAI]


Click here to see an example

Click here to see an example


Protein alignment:

Use this option to calculate the Codon Adaptation Index (CAI) from a protein alignment that has been translated to a DNA alignment using (a) a unique codon usage table as a reference or (b) multiple codon usage tables as a reference.


[One reference table]

[Multiple reference tables]


Click here to see an example

Click here to see an example




TUTORIAL     FAQs     Local Version

For comments, suggestions or questions please send an e-mail to Pere Puigbo (ppuigbo AT urv.net) or Santi Garcia-Vallve (santi.garcia-vallve AT urv.net). Please put 'CAIcal' as a subject.

This Server were financied by:

Ref. BIO2003-07672

Powered by Apache server Powered by PHP