Affiliation: University of Vigo
- Parallel evolution of the genetic code in arthropod mitochondrial genomesFederico 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...
- Genetic code prediction for metazoan mitochondria with GenDecoderFederico 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...
- ProtTest: selection of best-fit models of protein evolutionFederico 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. AVAILABILITY: ProtTest is available under the GNU license from http://darwin.uvigo.es..
- GenDecoder: genetic code prediction for metazoan mitochondriaFederico 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...
- Clustering of proximal sequence space for the identification of protein familiesFederico Abascal
Protein Design Group, National Centre for Biotechnology, CNB-CSIC, Cantoblanco, Madrid E-28049, Spain
Bioinformatics 18:908-21. 2002..AVAILABILITY: The analysis of different systems, including the COG equivalent 21 genomes are available at http://www.pdg.cnb.uam.es/GenoClustering.html...
- Automatic annotation of protein function based on family identificationFederico 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...
- MtArt: a new model of amino acid replacement for ArthropodaFederico Abascal
Mol Biol Evol 24:1-5. 2007....
- ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip dataFederico 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..