P. Janssen, B. Audit, I. Cases, N. Darzentas, L. Goldovsky et al., Beyond 100 genomes, Genome Biology, vol.4, issue.5, p.402, 2003.
DOI : 10.1186/gb-2003-4-5-402

M. Andrade and C. Sander, Bioinformatics: from genome data to biological knowledge, Current Opinion in Biotechnology, vol.8, issue.6, pp.675-683, 1997.
DOI : 10.1016/S0958-1669(97)80118-8

P. Karp, What we do not know about sequence analysis and sequence databases, Bioinformatics, vol.14, issue.9, pp.753-754, 1998.
DOI : 10.1093/bioinformatics/14.9.753

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/14/9/753

W. Pearson, [5] Rapid and sensitive sequence comparison with FASTP and FASTA, Methods Enzymol, vol.183, pp.63-98, 1990.
DOI : 10.1016/0076-6879(90)83007-V

S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990.
DOI : 10.1016/S0022-2836(05)80360-2

S. Altschul, T. Madden, A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

A. Krogh, M. Brown, I. Mian, K. Sjolander, and D. Haussler, Hidden Markov Models in Computational Biology, Journal of Molecular Biology, vol.235, issue.5, pp.1501-1531, 1994.
DOI : 10.1006/jmbi.1994.1104

S. Vinga and J. Almeida, Alignment-free sequence comparison--a review, Bioinformatics, vol.19, issue.4, pp.513-523, 2003.
DOI : 10.1093/bioinformatics/btg005

J. Vries, R. Munshi, D. Tobi, J. Klein-seetharaman, and P. Benos, A Sequence Alignment-Independent Method for Protein Classification, Applied Bioinformatics, vol.26, issue.39, pp.137-148, 2004.
DOI : 10.2165/00822942-200403020-00008

F. Abascal and A. Valencia, Automatic annotation of protein function based on family identification, Proteins: Structure, Function, and Genetics, vol.290, issue.3, pp.683-692, 2003.
DOI : 10.1002/prot.10449

W. Krebs and P. Bourne, Statistically rigorous automated protein annotation, Bioinformatics, vol.20, issue.7, pp.1066-1073, 2004.
DOI : 10.1093/bioinformatics/bth039

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.2.8227

A. Leontovich, L. Brodsky, V. Drachev, and V. Nikolaev, Adaptive algorithm of automated annotation, Bioinformatics, vol.18, issue.6, pp.838-844, 2002.
DOI : 10.1093/bioinformatics/18.6.838

R. Tatusov, M. Galperin, D. Natale, and E. Koonin, The COG database: a tool for genome-scale analysis of protein functions and evolution, Nucleic Acids Research, vol.28, issue.1, pp.33-36, 2000.
DOI : 10.1093/nar/28.1.33

M. Ashburner, C. Ball, J. Blake, D. Botstein, H. Butler et al., Gene Ontology: tool for the unification of biology, Nature Genetics, vol.9, issue.1, pp.25-29, 2000.
DOI : 10.1038/75556

A. Gattiker, K. Michoud, C. Rivoire, A. Auchincloss, E. Coudert et al., Automated annotation of microbial proteomes in SWISS-PROT, Computational Biology and Chemistry, vol.27, issue.1, pp.49-58, 2003.
DOI : 10.1016/S1476-9271(02)00094-4

D. Wieser, E. Kretschmann, and R. Apweiler, Filtering erroneous protein annotation, Bioinformatics, vol.20, issue.Suppl 1, pp.342-347, 2004.
DOI : 10.1093/bioinformatics/bth938

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/20/suppl_1/i342

A. Murzin, S. Brenner, T. Hubbard, and C. Chothia, SCOP: A structural classification of proteins database for the investigation of sequences and structures, Journal of Molecular Biology, vol.247, issue.4, pp.536-540, 1995.
DOI : 10.1016/S0022-2836(05)80134-2

L. Holm and C. Sander, Mapping the Protein Universe, Science, vol.273, issue.5275, pp.595-603, 1996.
DOI : 10.1126/science.273.5275.595

T. Jaakkola, M. Diekhans, and D. Haussler, A Discriminative Framework for Detecting Remote Protein Homologies, Journal of Computational Biology, vol.7, issue.1-2, pp.95-114, 2000.
DOI : 10.1089/10665270050081405

B. Boeckmann, A. Bairoch, R. Apweiler, M. Blatter, A. Estreicher et al., The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003, Nucleic Acids Research, vol.31, issue.1, pp.365-370, 2003.
DOI : 10.1093/nar/gkg095

V. Promponas, A. Enright, S. Tsoka, D. Kreil, C. Leroy et al., CAST: an iterative algorithm for the complexity analysis of sequence tracts, Bioinformatics, vol.16, issue.10, pp.915-922, 2000.
DOI : 10.1093/bioinformatics/16.10.915