Prediction of Protein Function - Genomics: Essential Methods - page 206

57. Thompson, J.D., Plewniak, F., Ripp, R. et al . (2001) Towards a reliable objective function for
multiple sequence alignments. Journal of Molecular Biology , 314 , 937-951.
58. Altschul, S.F., Madden, T.L., Schaffer, A.A. et al . (1997) Gapped BLAST and PSI-BLAST: a
new generation of protein database search programs. Nucleic Acids Research , 25 , 3389-3402.
PSI-BLAST extends conventional BLAST to retrieve the homologues of a protein with much
lower sequence similarity.
59. Date, S.V. and Marcotte, E.M. (2003) Discovery of uncharacterized cellular systems by
genome-wide analysis of functional linkages. Nature Biotechnology , 21 , 1055-1062.
60. Sun, J., Li, Y. and Zhao, Z. (2007) Phylogenetic profiles for the prediction of protein-protein
interactions: how to select reference organisms? Biochemical and Biophysical Research , 353 ,
985-991.
61. Woese, C.R., Kandler, O. and Wheelis, M.L. (1990) Towards a natural system of organisms:
proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy
of Sciences of the United States of America , 87 , 4576-4579.
62. Vert, J.P. (2002) A tree kernel to analyse phylogenetic profiles. Bioinformatics , 18 (Suppl. 1),
S276-S284.
63. Barker, D., Meade, A. and Pagel, M. (2007) Constrained models of evolution lead to improved
prediction of functional linkage from correlated gain and loss of genes. Bioinformatics , 23 , 14-20.
64. Barker, D. and Pagel, M. (2005) Predicting functional gene links from phylogenetic-statistical
analyses of whole genomes. PLoS Computational Biology , 1 ,e3.
65. Natale, D.A., Galperin, M.Y., Tatusov, R.L. and Koonin, E.V. (2000) Using the COG database
to improve gene recognition in complete genomes. Genetica , 108 , 9-17.
66. Cokus, S., Mizutani, S. and Pellegrini, M. (2007) An improved method for identifying functionally
linked proteins using phylogenetic profiles. BMC Bioinformatics , 8 (Suppl. 4), S7.
67. Eisen, J.A. (1998) Phylogenomics: improving functional predictions for uncharacterized genes by
evolutionary analysis. Genome Research , 8 , 163-167.
68. Engelhardt, B.E., Jordan, M.I., Muratore, K.E. and Brenner, S.E. (2005) Protein molecular function
prediction by Bayesian phylogenomics. PLoS Computational Biology , 1 , e45.
69. Zmasek, C.M. and Eddy, S.R. (2002) RIO: analyzing proteomes by automated phylogenomics
using resampled inference of orthologs. BMC Bioinformatics , 3 , 14.
70. Lobley, A.E., Nugent, T., Orengo, C.A. and Jones, D.T. (2008) FFPred: an integrated feature-based
function prediction server for vertebrate proteomes. Nucleic Acids Research , 36 , W297-W302.
71. Jensen, L.J., Gupta, R., Staerfeldt, H.H. and Brunak, S. (2003) Prediction of human protein
function according to Gene Ontology categories. Bioinformatics , 19 , 635-642.
72. Cai, C.Z., Han, L.Y., Ji, Z.L. et al . (2003) SVM-Prot: web-based support vector machine software
for functional classification of a protein from its primary sequence. Nucleic Acids Research , 31 ,
3692-3697.
73. Lobley, A., Swindells, M.B., Orengo, C.A. and Jones, D.T. (2007) Inferring function using patterns
of native disorder in proteins. PLoS Computational Biology , 3 , e162. This publication describes
the use of a large variety of sequence-derived biochemical properties of proteins with SVMs for
function inference.
74. Ward, J.J., McGuffin, L.J., Bryson, K. et al . (2004) The DISOPRED server for the prediction of
protein disorder. Bioinformatics , 20 , 2138-2139.