Federico Abascal

Summary

Affiliation: University of Vigo
Country: Spain

Publications

  1. pmc Parallel evolution of the genetic code in arthropod mitochondrial genomes
    Federico Abascal
    Departamento de Bioquimica, Genetica, e Inmunología, Universidad de Vigo, Vigo, Spain
    PLoS Biol 4:e127. 2006
  2. doi Genetic code prediction for metazoan mitochondria with GenDecoder
    Federico Abascal
    Departamento de Genetica, Bioquímica e Inmunología, Facultad de Biologia, Universidad de Vigo, Vigo, Spain
    Methods Mol Biol 537:233-42. 2009
  3. ncbi ProtTest: selection of best-fit models of protein evolution
    Federico Abascal
    Department of Biochemistry, Genetics and Immunology, Universidad de Vigo, Spain
    Bioinformatics 21:2104-5. 2005
  4. pmc GenDecoder: genetic code prediction for metazoan mitochondria
    Federico Abascal
    Departamento de Bioquimica, Genetica, e Inmunología, Universidad de Vigo, 36310 Vigo, Spain
    Nucleic Acids Res 34:W389-93. 2006
  5. ncbi Clustering of proximal sequence space for the identification of protein families
    Federico Abascal
    Protein Design Group, National Centre for Biotechnology, CNB CSIC, Cantoblanco, Madrid E 28049, Spain
    Bioinformatics 18:908-21. 2002
  6. ncbi Automatic annotation of protein function based on family identification
    Federico Abascal
    Protein Design Group, National Centre for Biotechnology, CNB CSIC, Cantoblanco, Madrid, Spain
    Proteins 53:683-92. 2003
  7. ncbi MtArt: a new model of amino acid replacement for Arthropoda
    Federico Abascal
    Mol Biol Evol 24:1-5. 2007
  8. doi ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data
    Federico Abascal
    Biocomputing Unit, National Center of Biotechnology CSIC, Madrid, Spain
    Bioinformatics 24:1208-9. 2008

Detail Information

Publications8

  1. pmc Parallel evolution of the genetic code in arthropod mitochondrial genomes
    Federico Abascal
    Departamento de Bioquimica, Genetica, e Inmunología, Universidad de Vigo, Vigo, Spain
    PLoS Biol 4:e127. 2006
    ..These rather simple mutations, together with a low usage of the AGG codon, might explain the recurrence of the AGG reassignments...
  2. doi Genetic code prediction for metazoan mitochondria with GenDecoder
    Federico Abascal
    Departamento de Genetica, Bioquímica e Inmunología, Facultad de Biologia, Universidad de Vigo, Vigo, Spain
    Methods Mol Biol 537:233-42. 2009
    ..uvigo.es/software/gendecoder.html). In this chapter we describe the rationale of the method used by GenDecoder and its usage through worked examples, highlighting the potential problems that can arise during the analysis...
  3. ncbi ProtTest: selection of best-fit models of protein evolution
    Federico Abascal
    Department of Biochemistry, Genetics and Immunology, Universidad de Vigo, Spain
    Bioinformatics 21:2104-5. 2005
    ..We have built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment...
  4. pmc GenDecoder: genetic code prediction for metazoan mitochondria
    Federico Abascal
    Departamento de Bioquimica, Genetica, e Inmunología, Universidad de Vigo, 36310 Vigo, Spain
    Nucleic Acids Res 34:W389-93. 2006
    ..Overall, the method is highly precise (99%), although highly divergent organisms such as platyhelminths are more problematic. The GenDecoder web server is freely available from http://darwin.uvigo.es/software/gendecoder.html...
  5. ncbi Clustering of proximal sequence space for the identification of protein families
    Federico Abascal
    Protein Design Group, National Centre for Biotechnology, CNB CSIC, Cantoblanco, Madrid E 28049, Spain
    Bioinformatics 18:908-21. 2002
    ..These problems are the motivation for the development of methods for clustering protein sequences and building families of potentially orthologous sequences, such as those proposed here...
  6. ncbi Automatic annotation of protein function based on family identification
    Federico Abascal
    Protein Design Group, National Centre for Biotechnology, CNB CSIC, Cantoblanco, Madrid, Spain
    Proteins 53:683-92. 2003
    ..Results can be accessed at http://www.pdg.cnb.uam.es/funcut.html. The programs are available upon request, although installation in other systems may be complicated...
  7. ncbi MtArt: a new model of amino acid replacement for Arthropoda
    Federico Abascal
    Mol Biol Evol 24:1-5. 2007
    ....
  8. doi ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data
    Federico Abascal
    Biocomputing Unit, National Center of Biotechnology CSIC, Madrid, Spain
    Bioinformatics 24:1208-9. 2008
    ..For a given list of yeast genes ChIPCodis determines which combinations of TFs are significantly over-represented in a series of environmental conditions. Availability: http://chipcodis.dacya.ucm.es..