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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. |
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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. |
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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. |
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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. |
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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:
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