Detecting species-site dependencies in large multiple sequence alignments

Nucleic Acids Research

Volumn 37, Issue 18, 2009, Pages 5959-5968

  Schwarz, Roland ^a,b   Seibel, Philipp N ^b   Rahmann, Sven ^c   Schoen, Christoph ^a   Huenerberg, Mirja ^b   Müller reible, Clemens ^b   Dandekar, Thomas ^b   Karchin, Rachel ^d   Schultz, Jörg ^b   Müller, Tobias ^b  

^a UNIVERSITY OF WÜRZBURG   (Germany)

^b UNIVERSITY OF WÜRZBURG   (Germany)

^c TU DORTMUND UNIVERSITY   (Germany)

^d Johns Hopkins University School of Medicine   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; NEISSERIA MENINGITIDIS FACTOR H BINDING PROTEIN; OXIDOREDUCTASE; UNCLASSIFIED DRUG; VITAMIN K EPOXIDE REDUCTASE;

ARTICLE; GENE CLUSTER; GENE INSERTION; GENE LOCATION; GENE MAPPING; GENE MUTATION; GENE SEQUENCE; GENE TRANSFER; MULTIPLE SEQUENCE ALIGNMENT; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROBABILITY; PROTEIN MOTIF; SCORING SYSTEM; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION;

ANTIGENS, BACTERIAL; BACTERIAL PROTEINS; MIXED FUNCTION OXYGENASES; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

NEISSERIA;

EID: 70350643834     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp634     Document Type: Article

References (50)

1. Galtier,N., Gouy,M. and Gautier,C. (1996) SEAVIEW and PHYLO-WIN: Two graphic tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci., 12, 543-548.
2. Thompson,J.D., Gibson,T.J., Plewniak,F., Jeanmougin,F. and Higgins,D.G. (1997) The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 25, 4876-4882.
3. Clamp,M., Cuff,J., Searle,S.M. and Barton,G.J. (2004) The Jalview Java alignment editor. Bioinformatics, 20, 426-427.
4. Seibel,P.N., Müller,T., Dandekar,T. and Wolf,M. (2008) Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE. BMC Res. Notes, 1, 91.
5. Schneider,T.D. and Stephens,R.M. (1990) Sequence logos: A new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100.
6. Gorodkin,J., Heyer,L.J., Brunak,S. and Stormo,G.D. (1997) Displaying the information contents of structural RNA alignments: The structure logos. Comput. Appl. Biosci., 13, 583-586.
7. Chang,T.-H., Horng,J.-T. and Huang,H.-D. (2008) RNALogo: A new approach to display structural RNA alignment. Nucleic Acids Res., 36, W91-W96.
8. Churchill,G.A. (1992) Hidden Markov-chains and the analysis of genome structure. Comput. Chem., 16, 107-115.
9. Krogh,A., Brown,M., Mian,I.S., Sjölander,K. and Haussler,D. (1994) Hidden Markov models in computational biology. Applications to protein modeling. J. Mol. Biol., 235, 1501-1531.
10. Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
11. Schuster-Böckler,B., Schultz,J. and Rahmann,S. (2004) HMM Logos for visualization of protein families. BMC Bioinformatics, 5, 7.
12. Hughey,R., Karplus,K. and Krogh,A. (2003) SAM Sequence alignment and modeling software system. Technical Report UCSC-CRL-99-11. Update for SAM Version 3.4, Baskin School of Engineering, University of California, Santa Cruz.
13. Casari,G., Sander,C. and Valencia,A. (1995) A method to predict functional residues in proteins. Nat. Struct. Biol., 2, 171-178.
14. Jaakkola,T., Diekhans,M. and Haussler,D. (2000) A discriminative framework for detecting remote protein homologies. J. Comput. Biol. 7, 95-114.
15. Jaakkola,T., Diekhans,M. and Haussler,D. (1999) Using the Fisher kernel method to detect remote protein homologies. Proc. Int. Conf. Intell. Syst. Mol. Biol., 149-158.
16. Karchin,R., Karplus,K. and Haussler,D. (2002) Classifying G-protein coupled receptors with support vector machines. Bioinformatics, 18, 147-159.
17. Legendre,P. and Legendre,L. (1998) Numerical Ecology. Elsevier.
18. Jaakkola,T.S. and Haussler,D. (1998) Exploiting generative models in discriminative classifiers. Adv. Neural Inf. Process. Syst., 11 487-493.
19. Shawe-Taylor,J. and Cristianini,N. (2004) Kernel Methods for Pattern Analysis. Cambridge University Press.
20. Golub,G.H. and vanLoan,C.F. (1996) Matrix Computations. The Johns Hopkins University Press.
21. Weller,S.C. and Romney,A.K. (1990) Metric Scaling - Correspondence Analysis. SAGE.
22. Edgar,R.C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
23. Friedrich,J., Dandekar,T., Wolf,M. and Müller,T. (2005) ProfDist: A tool for the construction of large phylogenetic trees based on profile distances. Bioinformatics, 21, 2108-2109.
24. Wolf,M., Ruderisch,B., Dandekar,T., Schultz,J. and Müller,T. (2008) ProfDistS: (profile-) distance based phylogeny on sequencestructure alignments. Bioinformatics, 24, 2401-2402.
25. Müller,T. and Vingron,M. (2000) Modeling amino acid replacement. J. Comput. Biol., 7, 761-776.
26. Huson,D.H. and Bryant,D. (2006) Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol., 23, 254-267.
27. Altschul,S.F., Madden,T.L., Schffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSIBLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
28. Birney,E., Clamp,M. and Durbin,R. (2004) GeneWise and Genomewise. Genome Res., 14, 988-995.
29. Felsenstein,J. (2005) PHYLIP (Phylogeny Inference Package) version 3.6, (distributed by the author). Department of Genome Sciences, University of Washington, Seattle.
30. Yang,Z. (2007) PAML 4: Phylogenetic analysis by maximum likelihood. Mol. Biol. Evol., 24, 1586-1591.
31. Fellenberg,K., Hauser,N.C., Brors,B., Neutzner,A., Hoheisel,J.D. and Vingron,M. (2001) Correspondence analysis applied to microarray data. Proc. Natl Acad. Sci. USA, 98, 10781-10786.
32. Masignani,V., Comanducci,M., Giuliani,M.M., Bambini,S., Adu-Bobie,J., Arico,B., Brunelli,B., Pieri,A., Santini,L., Savino,S. et al. (2003) Vaccination against Neisseria meningitidis using three variants of the lipoprotein GNA1870. J. Exp. Med., 197, 789-799.
33. Fletcher,L.D., Bernfield,L., Barniak,V., Farley,J.E., Howell,A., Knauf,M., Ooi,P., Smith,R.P., Weise,P., Wetherell,M. et al. (2004) Vaccine potential of the Neisseria meningitidis 2086 lipoprotein. Infect. Immun., 72, 2088-2100.
34. Giuliani,M.M., Adu-Bobie,J., Comanducci,M., Aric,B., Savino,S., Santini,L., Brunelli,B., Bambini,S., Biolchi,A., Capecchi,B. et al. (2006) A universal vaccine for serogroup B meningococcus. Proc. Natl Acad. Sci. USA, 103, 10834-10839.
35. Bruen,T.C., Philippe,H. and Bryant,D. (2006) A simple and robust statistical test for detecting the presence of recombination. Genetics, 172, 2665-2681.
36. Shearer,M.J. (2000) Role of vitamin K and Gla proteins in the pathophysiology of osteoporosis and vascular calcification. Curr. Opin. Clin. Nutr. Metab. Care, 3, 433-438.
37. Saxena,S.P., Israels,E.D. and Israels,L.G. (2001) Novel vitamin K-dependent pathways regulating cell survival. Apoptosis, 6, 57-68.
38. Furie,B., Bouchard,B.A. and Furie,B.C. (1999) Vitamin K-dependent biosynthesis of gamma-carboxyglutamic acid. Blood, 93, 1798-1808.
39. Wajih,N., Hutson,S.M. and Wallin,R. (2007) Disulfide-dependent protein folding is linked to operation of the vitamin K cycle in the endoplasmic reticulum. A protein disulfide isomerase-VKORC1 redox enzyme complex appears to be responsible for vitamin K1 2,3-epoxide reduction. J. Biol. Chem., 282, 2626-2635.
40. Cain,D., Hutson,S.M. and Wallin,R. (1998) Warfarin resistance is associated with a protein component of the vitamin K 2,3-epoxide reductase enzyme complex in rat liver. Thromb. Haemost., 80, 128-133.
41. Oldenburg,J., vonBrederlow,B., Fregin,A., Rost,S., Wolz,W., Eberl,W., Eber,S., Lenz,E., Schwaab,R., Brackmann,H.H. et al. (2000) Congenital deficiency of vitamin K dependent coagulation factors in two families presents as a genetic defect of the vitamin K-epoxide-reductase-complex. Thromb. Haemost., 84, 937-941.
42. Pelz,H.-J., Rost,S., Hünerberg,M., Fregin,A., Heiberg,A.-C., Baert,K., MacNicoll,A.D., Prescott,C.V., Walker,A.-S., Oldenburg,J. et al. (2005) The genetic basis of resistance to anticoagulants in rodents. Genetics, 170, 1839-1847.
43. Fregin,A., Rost,S., Wolz,W., Krebsova,A., Müller,C.R. and Oldenburg,J. (2002) Homozygosity mapping of a second gene locus for hereditary combined deficiency of vitamin K-dependent clotting factors to the centromeric region of chromosome 16. Blood, 100, 3229-3232.
44. Tie,J.-K., Nicchitta,C., vonHeijne,G. and Stafford,D.W. (2005) Membrane topology mapping of vitamin K epoxide reductase by in vitro translation/ cotranslocation. J. Biol. Chem., 280, 16410-16416.
45. Rost,S., Fregin,A., Ivaskevicius,V., Conzelmann,E., Hürtnagel,K., Pelz,H.-J., Lappegard,K., Seifried,E., Scharrer,I., Tuddenham,E.G.D. et al. (2004) Mutations in VKORC1 cause warfarin resistance and multiple coagulation factor deficiency type 2. Nature, 427, 537-541.
46. Li,T., Chang,C.-Y., Jin,D.-Y., Lin,P.-J., Khvorova,A. and Stafford,D.W. (2004) Identification of the gene for vitamin K epoxide reductase. Nature, 427, 541-544.
47. Brown,M., Hughey,R., Krogh,A., Mian,I.S., Sjlander,K. and Haussler,D. (1993) Using Dirichlet mixture priors to derive hidden Markov models for protein families. Proc. Int. Conf. Intell. Syst. Mol. Biol., 1 47-55.
48. Sjlander,K., Karplus,K., Brown,M., Hughey,R., Krogh,A., Mian,I.S. and Haussler,D. (1996) Dirichlet mixtures: A method for improved detection of weak but significant protein sequence homology. Comput. Appl. Biosci., 12, 327-345.
49. Durbin,R., Eddy,S., Krogh,A. and Mitchison,G. (1998) Biological Sequence Analysis. Cambridge University Press.
50. Waterhouse,A.M., Procter,J.B., Martin,D.M.A., Clamp,M. and Barton,G.J. (2009) Jalview Version 2 - a multiple sequence alignment editor and analysis workbench. Bioinformatics, 25, 1189-1191.