Databases and tools available at genomes.urv.cat

Bioinformatics databases and web tools developed at Universitat Rovira i Virgili

OPTIMIZER

Author: Pere Puigbò and Santi Garcia‑Vallvé

OPTIMIZER is an online application that optimizes codon usage of DNA sequences to increase expression levels.

P. Puigbò, E. Guzman, A. Romeu and S. Garcia‑Vallvé (2007). OPTIMIZER: A web server for optimizing the codon usage of DNA sequences. Nucleic Acids Research, 35(Web Server issue): W126‑W131.

Open tool

DendroUPGMA

Author: Santi Garcia‑Vallvé

Create dendrograms from sets of variables using the UPGMA clustering algorithm.

S. Garcia‑Vallvé, J. Palau and A. Romeu (1999). Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis. Molecular Biology and Evolution, 16:1125‑1134.

Open tool

CAIcal / E-CAI / RCDI

Author: Pere Puigbò

Calculates Codon Adaptation Index (CAI), an expected value (E-CAI) and other parameters related to codon usage and codon adaptation of gene sequences.

Puigbo P, Bravo IG and Garcia‑Vallve S. (2008). CAIcal: a combined set of tools to assess codon usage adaptation. Biology Direct 3:38. doi: 10.1186/1745-6150-3-38

Open tool

Horizontal Gene Transfer Database (HGT‑DB)

Author: Santi Garcia‑Vallvé

Database of putative horizontally transferred genes in prokaryotic genomes.

S. Garcia‑Vallve, E. Guzman, M.A. Montero and A. Romeu. (2003). HGT‑DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Research, 31:187‑189.

Not available anymore See an older version

Highly Expressed Genes Database (HEG‑DB)

Author: Pere Puigbò

Database of predicted highly expressed genes in prokaryotic genomes under translational selection.

Puigbo P, Romeu A and Garcia‑Vallve S. (2008). HEG‑DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection. Nucleic Acids Research, 36(Database issue): D524‑D527. doi:10.1093/nar/gkm831.

Not available anymore