Detection of conserved domains in protein sequences using a maximum-density subgraph algorithm

IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences

Volumn E83-A, Issue 4, 2000, Pages 713-721

  Matsuda, Hideo ^a  

^a OSAKA UNIVERSITY   (Japan)

Author keywords

Approximate string comparison; Computational molecular biology; Maximum flow algorithm; Maximum density subgraph; Protein sequence analysis

Indexed keywords

ALGORITHMS; PROTEINS;

MAXIMUM-DENSITY SUBGRAPH ALGORITHMS;

GRAPH THEORY;

EID: 0033700928     PISSN: 09168508     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (44)

1. W.M. Fitch, "Distinguishing homologous from analogous proteins," Systematic Zoology, vol.19, no.2, pp.99-113, 1970.
2. E.V. Koonin, R.L. Tatusov, and K.E. Rudd, "Sequence similarity analysis of Escherichia coli proteins - functional and evolutionary implications," Proc. Natl. Acad. Sci. USA, vol.92, pp.11921-11925, 1995.
3. H. Watanabe and J. Otsuka, "A comprehensive representation of extensive similarity linkage between large numbers of proteins," Computer Applications in Biosciences, vol.11, no.2, pp.159-166, 1995.
4. M. Riley and B. Labeden, "Protein evolution viewed through Escherichia coli protein sequences: Introducing the notion of a structural segment of homology, the module," J. Molecular Biology, vol.268, pp.857-868, 1997.
5. S. Henikoff, E.A. Greene S. Pietrokovski, P. Bork, T.K. Attwood, and L. Hood, "Gene families: the taxonomy of protein paralogs and chimeras," Science, vol.278, pp.609-614, 1997.
6. H. Matsuda, T. Ishihara, and A. Hashimoto, "Classifying molecular sequences using a linkage graph with their pair-wise similarities," Theoretical Computer Science, vol.210, no.2, pp.305-325, 1999.
7. S.M. Soisson, B. MacDougall-Shackleton, R. Schleif, and C. Wolberger, "Structural basis for ligand-regulated oligomerization of AraC," Science, vol.276, no.5311, pp.421-425, 1997.
8. M. Lewis, et al., "Crystal structure of the lactose operon repressor and its complexes with DNA and inducer," Science, vol.271, no.5253, pp.1247-1254, 1996.
9. A.J. Bjorkman, et al., "Probing protein-protein interactions: the ribose binding protein in bacterial transport and chemotaxis," J. Biol. Chem., vol.269, no.48, pp.30206-30211, 1994.
10. A. Bairoch and R. Apweiler, "The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999," Nucleic Acids Research, vol.27, no.1, pp.49-54, 1999.
11. R.L. Tatusov, S.F. Altschul, and E.V. Koonin, "Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks," Proc. Natl. Acad. Sci. USA, vol.91, pp.12091-12095, 1994.
12. E.L.L. Sonnhammer and D. Kahn, "Modular arrangement of proteins as inferred from analysis of homology," Protein Science, vol.3, pp.482-492, 1994.
13. S. Suharnan, T. Itoh, H. Matsuda, and H. Mori, "Clustering molecular sequences with their components," Genome Informatics 1997, Genome Informatics Series no.8, pp.125-134, Universal Academy Press, Tokyo, 1997.
14. J. Gracy and P. Argos, "Automated protein sequence database classification. I. integration of compositional similarity search, local similarity search, and multiple sequence alignment," Bioinformatics, vol.14, no.2, pp.164-173, 1998.
15. J. Gracy and P. Argos, "Automated protein sequence database classification. II. delineation of domain boundaries from sequence similarities," Bioinformatics, vol.14, no.2, pp.174-187, 1998.
16. J. Park and S.A. Teichmann, "DIVCLUS: An automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins," Bioinformatics, vol.14, no.2, pp.144-150, 1998.
17. M.O. Dayhoff, R.M. Schwartz, and B.C. Orcutt, "A model of evolutionary change in proteins," in Atlas of Protein Sequence and Structure, ed. M.O. Dayhoff, vol.5, no.3, pp.345-352, National Biomedical Research Foundation, Washington D.C., 1978.
18. S. Henikoff and J.G. Henikoff, "Amino acid substitution matrices from protein blocks," Proc. Natl. Acad. Sci. USA, vol.89, pp.10915-10919, 1992.
19. P. Bork, C. Sander, and A. Valencia, "An ATPase domain common to prokaryotic cell cycles proteins, sugar kinases, actin, and hsp70 heat shock proteins," Proc. Natl. Acad. Sci. USA, vol.89, pp.7290-7294, 1992.
20. D.A. Benson, M.S. Boguski, D.J. Lipman, J. Ostell, B.F. Ouellette, B.A. Rapp, and D.L. Wheeler, "GenBank," Nucleic Acid Research, vol.27, no.l, pp.12-17, 1999.
21. F.R. Blattner, et al., "The complete genome sequence of Escherichia colt K-12," Science, vol.277, no.5331, pp.1453-1474, 1997.
22. W.R. Pearson and D.J. Lipman, "Improved tools for biological sequence comparison," Proc. Natl. Acad. Sci. USA, vol.85, pp.2444-2448, 1988.
23. G. Gallo, M.D. Grigoriadis, and R.E. Tarjan, "A fast parametric maximum flow algorithm and applications," SIAM J. Comput., vol.18, no.1, pp.30-55, 1989.
24. T. Mizuno, "Compilation of all genes encoding two-component phosphotransfer signal transducers on the genome of Escherichia coli" DNA Research, vol.4, pp. 161-168, 1997.
25. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman, "A basic local alignment search tool," J. Molecular Biology, vol.215, pp.403-410, 1990.
26. 70 family: Sequence conservation and evolutionary relationships," J. Bacteriology, vol.174, no.12, pp.3843-3849, 1992.
27. M.A. Lonetto, K.L. Brown, K.E. Rudd, and M.J. Buttner, "Analysis of the Streptomyces coelicolor sigE gene reveals the existence of a subfamily of eubacterial RNA polymerase σ factors involved in the regulation of extracytoplasmic functions," Proc. Natl. Acad. Sci. USA, vol.91, pp.7573-7577, 1994.
28. H.P. Klenk, et al., "The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus" Nature, vol.390, no.6658, pp.364-370, 1997.
29. G. Deckert, et al., "The complete genome of the hyperthermophilic bacterium Aquifex aeolicus" Nature, vol.392, no.6674, pp.353-358, 1998.
30. C.M. Fraser, et al., "Genomic sequence of a lyme disease spirochete, Borrelia burgdorferi," Nature, vol.390, no.6660, pp.580-586, 1997.
31. F. Kunst, et al., "The complete genome sequence of the gram-positive bacterium Bacillus subtilis," Nature, vol.390, no.6657, pp.249-256, 1997.
32. R.S. Stephens, et al., "Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis," Science, vol.282, pp.754-759, 1998.
33. R.D. Fleischmann, et al., "Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.," Science, vol.269, no.5223, pp.496-512, 1995.
34. J.-F. Tomb, et al., "The complete genomes sequence of the gastric pathogen Helicobacter pylori," Nature, vol.388, no.6642, pp.539-547, 1997.
35. D.R. Smith, et al., "Complete genome sequence of Methanobacterium thermoautotrophicum delta h: Functional analysis and comparative genomic," J. Bacteriology, vol.179, pp.7135-7155, 1997.
36. C.J. Bult, et al., "Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii" Science, vol.273, no.5278, pp.1058-1073, 1996.
37. S.T. Cole, et al., "Deciphering the biology of the tubercule bacillus: The complete genome sequence of Mycobacterium tuberculosis H37Rv," Nature, vol.393, no.6685, pp.537-544, 1998.
38. C.M. Fraser, et al., "The minimal gene complement of Mycoplasma genitalium," Science, vol.270, no.5235, pp.397-403, 1995.
39. R. Himmelreich, et al., "Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae," Nucleic Acids Research, vol.24, no.22, pp.4420-4449, 1996.
40. Y. Kawarabayasi, et al., "Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3," DNA Research, vol.5, pp.55-76, 1998.
41. T. Kaneko, et al., "Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions," DNA research, vol.3, no.3, pp. 109-136, 1996.
42. C.M. Fraser, et al., "Complete genome sequence of Treponema pallidum, the syphilis spirochete," Science, vol.281, pp.375-388, 1998.
43. K. Hofmann, P. Bucher, L. Falquet, and A. Bairoch, "The PROSITE database, its status in 1999," Nucleic Acids Research, vol.27, no.1, pp.215-219, 1997.
44. J.G. Henikoff, S. Henikoff, and S. Pietrokovski, "New features of the Blocks database servers," Nucleic Acids Research, vol.27, no.1, pp.226-228, 1999.