Pere Puigbò

Summary

Affiliation: Rovira i Virgili University
Country: Spain

Publications

  1. pmc HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection
    Pere Puigbò
    Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Faculty of Chemistry, Rovira i Virgili University URV, C Marcel li Domingo, s n Campus Sescelades, 43007 Tarragona, Spain
    Nucleic Acids Res 36:D524-7. 2008
  2. ncbi request reprint TOPD/FMTS: a new software to compare phylogenetic trees
    Pere Puigbò
    Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Rovira i Virgili University, Tarragona, Spain
    Bioinformatics 23:1556-8. 2007
  3. pmc E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI)
    Pere Puigbò
    Evolutionary Genomics Group, Department of Biochemistry and Biotechnology, Rovira i Virgili University URV, Campus Sescelades, c Marcelli Domingo s n, 43007 Tarragona, Spain
    BMC Bioinformatics 9:65. 2008
  4. pmc OPTIMIZER: a web server for optimizing the codon usage of DNA sequences
    Pere Puigbò
    Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Faculty of Chemistry, Rovira i Virgili University URV, Tarragona, Spain
    Nucleic Acids Res 35:W126-31. 2007
  5. pmc CAIcal: a combined set of tools to assess codon usage adaptation
    Pere Puigbò
    Department of Biochemistry and Biotechnology, Rovira i Virgili University URV, Campus Sescelades, c Marcelli Domingo s n, 43007 Tarragona, Spain
    Biol Direct 3:38. 2008
  6. ncbi request reprint Gaining and losing the thermophilic adaptation in prokaryotes
    Pere Puigbò
    Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Rovira i Virgili University URV, 43007 Tarragona, Spain
    Trends Genet 24:10-4. 2008
  7. pmc Towards reconstructing a metabolic tree of life
    Marina Marcet-Houben
    Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Rovira i Virgili University, Campus Sescelades, C Marcel li Domingo s n, 43007 Tarragona, Spain
    Bioinformation 2:135-44. 2007

Detail Information

Publications8

  1. pmc HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection
    Pere Puigbò
    Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Faculty of Chemistry, Rovira i Virgili University URV, C Marcel li Domingo, s n Campus Sescelades, 43007 Tarragona, Spain
    Nucleic Acids Res 36:D524-7. 2008
    ..The HEG-DB is freely available at http://genomes.urv.cat/HEG-DB...
  2. ncbi request reprint TOPD/FMTS: a new software to compare phylogenetic trees
    Pere Puigbò
    Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Rovira i Virgili University, Tarragona, Spain
    Bioinformatics 23:1556-8. 2007
    ..Each option is also complemented with a randomization analysis to test the null hypothesis that the similarity between two trees is not better than chance expectation...
  3. pmc E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI)
    Pere Puigbò
    Evolutionary Genomics Group, Department of Biochemistry and Biotechnology, Rovira i Virgili University URV, Campus Sescelades, c Marcelli Domingo s n, 43007 Tarragona, Spain
    BMC Bioinformatics 9:65. 2008
    ..Though several freely available programs calculate the CAI for a given DNA sequence, none of them corrects for compositional biases or provides confidence intervals for CAI values...
  4. pmc OPTIMIZER: a web server for optimizing the codon usage of DNA sequences
    Pere Puigbò
    Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Faculty of Chemistry, Rovira i Virgili University URV, Tarragona, Spain
    Nucleic Acids Res 35:W126-31. 2007
    ..OPTIMIZER is accessible free of charge at http://genomes.urv.es/OPTIMIZER...
  5. pmc CAIcal: a combined set of tools to assess codon usage adaptation
    Pere Puigbò
    Department of Biochemistry and Biotechnology, Rovira i Virgili University URV, Campus Sescelades, c Marcelli Domingo s n, 43007 Tarragona, Spain
    Biol Direct 3:38. 2008
    ..The CAI quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set...
  6. ncbi request reprint Gaining and losing the thermophilic adaptation in prokaryotes
    Pere Puigbò
    Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Rovira i Virgili University URV, 43007 Tarragona, Spain
    Trends Genet 24:10-4. 2008
    ..Our findings suggest several examples in which the capacity of thermophilic adaptation has been gained or lost over relatively short evolutionary periods throughout the evolution of prokaryotes...
  7. pmc Towards reconstructing a metabolic tree of life
    Marina Marcet-Houben
    Evolutionary Genomics Group, Biochemistry and Biotechnology Department, Rovira i Virgili University, Campus Sescelades, C Marcel li Domingo s n, 43007 Tarragona, Spain
    Bioinformation 2:135-44. 2007
    ..thermophilum and Clostridia, combined with other evidence, suggest that S. thermophilum may be re-classified as Firmicutes, Clostridia...