References
- Irie Y, Mattoo S, Yuk MH. The Bvg virulence control system regulates biofilm formation in Bordetella bronchiseptica. J Bacteriol. 2004 Sep;186(17):5692-8.
- Geric B, Rupnik M, Gerding DN, Grabnar M, Johnson S. Distribution of Clostridium difficile variant toxinotypes and strains with binary toxin genes among clinical isolates in an American hospital. J Med Microbiol. 2004 Sep; 53(Pt 9):887-94.
- Ethelberg S, Olsen KE, Scheutz F, Jensen C, Schiellerup P, Enberg J, Petersen AM, Olesen B, Gerner-Smidt P, Molbak K. Virulence factors for hemolytic uremic syndrome, Denmark. Emerg Infect Dis. 2004 May;10(5):842-7.
- Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000 Jan 1;28(1):33-6.
- Hua S, Sun Z. Support vector machine approach for protein subcellular localization prediction. Bioinformatics. 2001 Aug;17(8):721-8.
- Bairoch A, Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 2000 Jan 1;28(1):45-8.
- Chothia C, Lesk AM. The relation between the divergence of sequence and structure in proteins. EMBO J. 1986 Apr;5(4):823-6.
- Rost B. Twilight zone of protein sequence alignments. Protein Eng. 1999 Feb;12(2):85-94.
- Karp PD. What we do not know about sequence analysis and sequence databases.
Bioinformatics. 1998;14(9):753-4.
- Hegyi H, Gerstein M. The relationship between protein structure and function: a comprehensive survey with application to the yeast genome.
J Mol Biol. 1999 Apr 23;288(1):147-64.
- Thornton JM, Orengo CA, Todd AE, Pearl FM. Protein folds, functions and evolution.
J Mol Biol. 1999 Oct 22;293(2):333-42. Review.
- des Jardins M, Karp PD, Krummenacker M, Lee TJ, Ouzounis CA. Prediction of enzyme classification from protein sequence without the use of sequence similarity.
Proc Int Conf Intell Syst Mol Biol. 1997;5:92-9.
- Shah I, Hunter L. Predicting enzyme function from sequence: a systematic appraisal.
Proc Int Conf Intell Syst Mol Biol. 1997;5:276-83.
- Li L, Shakhnovich EI, Mirny LA. Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases. Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4463-8. Epub 2003 Apr 04.
- Hannenhalli SS, Russell RB. Analysis and prediction of functional sub-types from protein sequence alignments.J Mol Biol. 2000 Oct 13;303(1):61-76.
- Joachims,T. (1999) Making large-scale SVM learning particle. In Scholkopf,B., Burges,C, and Smola,A.(eds), Advances in kernal Methods Support Vector Learning. MIT Pres, Cambridge, MA and London, pp 42-56.
- Brazma A, Jonassen I, Eidhammer I, Gilbert D. Approaches to the automatic discovery of patterns in biosequences. J Comput Biol. 1998 Summer;5(2):279-305.
- Barton GJ. Protein multiple sequence alignment and flexible pattern matching.
Methods Enzymol. 1990;183:403-28
- Gribskov M, McLachlan AD, Eisenberg D. Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci U S A. 1987 Jul;84(13):4355-8.
- Bowie JU, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 1991 Jul 12;253(5016):164-70.
- Luthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature. 1992 Mar 5;356(6364):83-5.
- Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402.
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403-10.
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