View - ResearchGate
View - ResearchGate View - ResearchGate
Sybil: Multiple Genome Comparison and Visualization 107References1. Remm, M., Storm, C. E., and Sonnhammer, E. L. (2001) Automatic clustering oforthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol. 314(5),1041–1052.2. Enright, A. J., Van Dongen, S., and Ouzounis, C. A. (2002) An efficient algorithmfor large-scale detection of protein families. Nucleic Acids Res. 30(7), 1575–1584.3. O’Brien, K. P., Remm, M., and Sonnhammer, E. L. (2005) Inparanoid: acomprehensive database of eukaryotic orthologs. Nucleic Acids Res. 33, D476–D480.4. Fujibuchi, W., Ogata, H., Matsuda, H., and Kanehisa, M. (2000) Automaticdetection of conserved gene clusters in multiple genomes by graph comparisonand P-quasi grouping. Nucleic Acids Res. 28(20), 4029–4036.5. Ogata, H., Fujibuchi, W., Goto, S., and Kanehisa, M. (2000) A heuristic graphcomparison algorithm and its application to detect functionally related enzymeclusters. Nucleic Acids Res. 28(20), 4021–4028.6. Li, L., Stoeckert, C. J., Jr., and Roos, D. S. (2003) OrthoMCL: identification ofortholog groups for eukaryotic genomes. Genome Res. 13(9), 2178–2179.7. Tatusov, R. L., Koonin, E. V., and Lipman, D. J. (1997) A genomic perspective onprotein families. Science 278, 631–637.8. Tatusov, R. L., Galperin, M. Y., Natale, D. A., and Koonin, E. V. (2000) The COGdatabase: a tool for genome-scale analysis of protein functions and evolution. NucleicAcids Res. 28, 33–36.9. Tatusov, R. L., Natale, D. A., Garkavtsev, I. V., et al. (2001) The COG database: newdevelopments in phylogenetic classification of proteins from complete genomes.Nucleic Acids Res. 29, 22–28.10. Jaccard, P. (1908) Nouvelles recherches sur la distribution florale. Bull. Soc.Vaud. Sci. Nat. 44, 223–270.11. Stajich, J. E., Block, D., Boulez, K., et al. (2002) The Bioperl toolkit: perl modulesfor the life sciences. Genome Res. 12(10), 1611–1618.12. Pan, X., Stein, L., and Brendel, V. (2005) SynBrowse: a synteny browser forcomparative sequence analysis. Bioinformatics 21(17), 3461–3468.13. Carver, T. J., Rutherford, K. M., Berriman, M., Rajandream, M. A., Barrell, B. G.,and Parkhill, J. (2005) ACT: the Artemis Comparison Tool. Bioinformatics21(16), 3422–3423.14. Lewis, S. E., Searle, S. M. J., Harris, N., et al. (2002) Apollo: a sequence annotationeditor. Genome Biol. 3(12), RESEARCH0082.15. Gish, W. (1996–2005) http://blast.wustl.edu.16. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basiclocal alignment search tool. J. Mol. Biol. 215(3), 403–410.17. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improvingthe sensitivity of progressive multiple sequence alignment through sequenceweighting, position-specific gap penalties and weight matrix choice. NucleicAcids Res. 22, 4673–4680.18. Cormen, T. H., Leiserson, C. E., Rivest, R. L., and Stein, C. (2001) MinimumSpanning Trees, in Introduction to Algorithms, 2nd ed., MIT Press and McGraw-Hill, pp. 561–579.
- Page 188: Prediction of ID and Its Use in Fun
- Page 192: Prediction of ID and Its Use in Fun
- Page 196: Prediction of ID and Its Use in Fun
- Page 200: Prediction of ID and Its Use in Fun
- Page 204: Prediction of ID and Its Use in Fun
- Page 208: IICOMPUTATIONAL METHODS II
- Page 212: 94 Crabtree et al.genomes, which is
- Page 216: 96 Crabtree et al.Fig. 2. Sybil pro
- Page 220: 98 Crabtree et al.Fig. 3. Computing
- Page 224: 100 Crabtree et al.3.1.5.1. FILTER
- Page 228: 102 Crabtree et al.3. For the sake
- Page 232: 104 Crabtree et al.Fig. 5. Best bid
- Page 236: 106 Crabtree et al.17. Some cluster
- Page 242: 7Estimating Protein Function Using
- Page 246: Estimating Protein Function Using P
- Page 250: Estimating Protein Function Using P
- Page 254: Estimating Protein Function Using P
- Page 258: Estimating Protein Function Using P
- Page 262: Estimating Protein Function Using P
- Page 266: Estimating Protein Function Using P
- Page 270: Estimating Protein Function Using P
- Page 274: Estimating Protein Function Using P
- Page 278: Estimating Protein Function Using P
- Page 282: 130 Davuluriinteracting proteins an
- Page 286: Table 1Web URLs of Promoter, TF Dat
Sybil: Multiple Genome Comparison and Visualization 107References1. Remm, M., Storm, C. E., and Sonnhammer, E. L. (2001) Automatic clustering oforthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol. 314(5),1041–1052.2. Enright, A. J., Van Dongen, S., and Ouzounis, C. A. (2002) An efficient algorithmfor large-scale detection of protein families. Nucleic Acids Res. 30(7), 1575–1584.3. O’Brien, K. P., Remm, M., and Sonnhammer, E. L. (2005) Inparanoid: acomprehensive database of eukaryotic orthologs. Nucleic Acids Res. 33, D476–D480.4. Fujibuchi, W., Ogata, H., Matsuda, H., and Kanehisa, M. (2000) Automaticdetection of conserved gene clusters in multiple genomes by graph comparisonand P-quasi grouping. Nucleic Acids Res. 28(20), 4029–4036.5. Ogata, H., Fujibuchi, W., Goto, S., and Kanehisa, M. (2000) A heuristic graphcomparison algorithm and its application to detect functionally related enzymeclusters. Nucleic Acids Res. 28(20), 4021–4028.6. Li, L., Stoeckert, C. J., Jr., and Roos, D. S. (2003) OrthoMCL: identification ofortholog groups for eukaryotic genomes. Genome Res. 13(9), 2178–2179.7. Tatusov, R. L., Koonin, E. V., and Lipman, D. J. (1997) A genomic perspective onprotein families. Science 278, 631–637.8. Tatusov, R. L., Galperin, M. Y., Natale, D. A., and Koonin, E. V. (2000) The COGdatabase: a tool for genome-scale analysis of protein functions and evolution. NucleicAcids Res. 28, 33–36.9. Tatusov, R. L., Natale, D. A., Garkavtsev, I. V., et al. (2001) The COG database: newdevelopments in phylogenetic classification of proteins from complete genomes.Nucleic Acids Res. 29, 22–28.10. Jaccard, P. (1908) Nouvelles recherches sur la distribution florale. Bull. Soc.Vaud. Sci. Nat. 44, 223–270.11. Stajich, J. E., Block, D., Boulez, K., et al. (2002) The Bioperl toolkit: perl modulesfor the life sciences. Genome Res. 12(10), 1611–1618.12. Pan, X., Stein, L., and Brendel, V. (2005) SynBrowse: a synteny browser forcomparative sequence analysis. Bioinformatics 21(17), 3461–3468.13. Carver, T. J., Rutherford, K. M., Berriman, M., Rajandream, M. A., Barrell, B. G.,and Parkhill, J. (2005) ACT: the Artemis Comparison Tool. Bioinformatics21(16), 3422–3423.14. Lewis, S. E., Searle, S. M. J., Harris, N., et al. (2002) Apollo: a sequence annotationeditor. Genome Biol. 3(12), RESEARCH0082.15. Gish, W. (1996–2005) http://blast.wustl.edu.16. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990) Basiclocal alignment search tool. J. Mol. Biol. 215(3), 403–410.17. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improvingthe sensitivity of progressive multiple sequence alignment through sequenceweighting, position-specific gap penalties and weight matrix choice. NucleicAcids Res. 22, 4673–4680.18. Cormen, T. H., Leiserson, C. E., Rivest, R. L., and Stein, C. (2001) MinimumSpanning Trees, in Introduction to Algorithms, 2nd ed., MIT Press and McGraw-Hill, pp. 561–579.