Gapped alignment of protein sequence motifs through Monte Carlo optimization of a hidden Markov model

BMC Bioinformatics

Volumn 5, Issue , 2004, Pages

  Neuwald, Andrew F ^a   Liu, Jun S ^b  

^a Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNMENT OPTIMIZATION; ENDOPLASMIC RETICULUM; FUNCTIONAL INFORMATION; MARKOV CHAIN MONTE CARLO; MONTE CARLO OPTIMIZATION; STATISTICAL FORMULATION; STRUCTURAL MECHANISMS; SUPPLEMENTARY INFORMATION;

AMINO ACIDS; CELL MEMBRANES; CHAINS; HIDDEN MARKOV MODELS; OPTIMIZATION;

PROTEINS;

ADENOSINE TRIPHOSPHATASE; GUANINE NUCLEOTIDE BINDING PROTEIN; PROLYL ENDOPEPTIDASE; PROTEIN P97; ARCHAEAL PROTEIN; BACTERIAL PROTEIN; GUANOSINE TRIPHOSPHATASE; HELMINTH PROTEIN; HYDROLASE; SERINE PROTEINASE;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; GENETIC CONSERVATION; MATHEMATICS; MITOCHONDRION; MONTE CARLO METHOD; PROBABILITY; PROCESS OPTIMIZATION; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN MOTIF; SEQUENCE ALIGNMENT; STATISTICAL ANALYSIS; STATISTICAL MODEL; THEORY; ANIMAL; CHEMISTRY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS; STATISTICS AND NUMERICAL DATA;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; ARCHAEAL PROTEINS; BACTERIAL PROTEINS; CONSERVED SEQUENCE; GTP PHOSPHOHYDROLASES; HELMINTH PROTEINS; HYDROLASES; MARKOV CHAINS; MOLECULAR SEQUENCE DATA; MONTE CARLO METHOD; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SERINE ENDOPEPTIDASES; SOFTWARE;

EID: 13244299130     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-5-157     Document Type: Article

References (35)

1. 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, 25(17): 389-3402.
2. Karplus K, Barrett C, Hughey R: Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998, 14(10):846-856.
3. Neuwald AF, Kannan N, Poleksic A, Hata N, Liu JS: Ran's C-terminal, basic patch and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras and Ran GTPases. Genome Res 2003, 13(4):673-692.
4. Liu JS, Neuwald AF, Lawrence CE: Bayesian models for multiple local sequence alignment and Gibbs sampling stragtegies. J Am Stat Assoc 1995, 90(432):1156-1170.
5. Neuwald AF, Liu JS, Lipman DJ, Lawrence CE: Extracting protein alignment models from the sequence database. Nucleic Acids Research 1997, 25(9):1665-1677.
6. Liu JS, Neuwald AF, Lawrence CE: Markovian structures in biological sequence alignments. J Am Stat Assoc 1999, 94: -15.
7. Altschul SF: Generalized affine gap costs for protein sequence alignment. Proteins 1998, 32(1):88-96.
8. Edgar RC: MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004, 5(1):113.
9. Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32(5): 792-1797. Print 2004
10. Katoh K, Misawa K, Kuma K, Miyata T: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002, 30(14):3059-3066.
11. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22(22):4673-4680.
12. Notredame C, Higgins DG, Heringa J: T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302(1):205-217.
13. Bahr A, Thompson JD, Thierry JC, Poch O: BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. Nucleic Acids Res 2001, 29(1):323-326.
14. Neuwald AF, Aravind L, Spouge JL, Koonin EV: AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res 1999, 9(1): 7-43.
15. Neuwald AF, Hirano T: HEAT repeats associated with condensins, cohesins, and other complexes involved in chromosome-related functions. Genome Research 2000, 10(10):1445-1452.
16. Neuwald AF, Poleksic A: PSI-BLAST searches using hidden markov models of structural repeats: prediction of an unusual sliding DNA clamp and of beta-propellers in UV-damaged DNA-binding protein. Nucleic Acids Res 2000, 28(18):3570-3580.
17. Hall A, ed: GTPases:. Oxford University Press; 2000.
18. Nardini M, Dijkstra BW: Alpha/beta hydrolase fold enzymes: the family keeps growing. Curr Opin Struct Biol 1999, 9(6): 32-737.
19. Ollis DL, Cheah E, Cygler M, Dijkstra B, Frolow F, Franken SM, Harel M, Remington SJ, Silman I, Schrag J: The alpha/beta hydrolase fold. Protein Eng 1992, 5:197-211.
20. Wang Q, Song C, Li CC: Molecular perspectives on p97-VCP: progress in understanding its structure and diverse biological functions. J Struct Biol 2004, 146(1-2):44-57.
21. Confalonieri F, Duguet M: A 200-amino acid ATPase module in search of a basic function. Bioessays 1995, 17(7): 39-650.
22. Swaffield JC, Melcher K, Johnston SA: A highly conserved ATPase protein as a mediator between acidic activation domains and the TATA-binding protein. Nature 1995, 374(6517):88-91.
23. Patel S, Latterich M: The AAA team: related ATPases with diverse functions. Trends Cell Biol 1998, 8(2):65-71.
24. Ogura T, Wilkinson AJ: AAA+ superfamily ATPases: common structure - diverse function. Genes Cells 2001, 6(7): 75-597.
25. Iyer LM, Leipe DD, Koonin EV, Aravind L: Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol 2004, 146(1-2):11-31.
26. Eddy SR: Profile hidden Markov models. Bioinformatics 1998, 14(9):755-763.
27. Hughey R, Krogh A: Hidden Markov models for sequence analysis: extension and analysis of the basic method. Comput Appl Biosci 1996, 12(2):95-107.
28. Liu JS: Monte Carlo Strategies in Scientific Computing. New York Springer-Verlag; 2001.
29. Kirkpatrick S, Gelatt CD, Vecchi MP: Optimization by simulated annealing. Science 1983, 220:671-680.
30. Neuwald AF, Liu JS, Lawrence CE: Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci 1995, 4:1618-1632.
31. Debenedetti PG, Stillinger FH: Supercooled liquids and the glass transition. Nature 2001, 410(6825):259-267.
32. Neuwald AF: Evolutionary clues to DNA polymerase III beta clamp structural mechanisms. Nucleic Acids Res 2003, 31(15): 503-4516.
33. Kannan N, Neuwald AF: Evolutionary constraints associated with functional specificity of the CMGC protein kinases MAPK, CDK, GSK, SRPK, DYRK, and CK2alpha. Protein Science 2004, 13: 00-000.
34. Zhang X, Shaw A, Bates PA, Newman RH, Gowen B, Orlova E, Gorman MA, Kondo H, Dokurno P, Lally J, Leonard G, Meyer H, van Heel M, Freemont PS: Structure of the AAA ATPase p97. Mol Cell 2000, 6(6):1473-1484.
35. Henikoff S, Henikoff JG: Position-based sequence weights. J Mol Biol 1994, 243:574-578.