COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance

Journal of Molecular Biology

Volumn 326, Issue 1, 2003, Pages 317-336

  Sadreyev, Ruslan ^a   Grishin, Nick ^a  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

CTF NFI; Profile profile comparison; Protein structure prediction; Sequence profiles; Sequence similarity searches

Indexed keywords

HELIX LOOP HELIX PROTEIN; SMAD PROTEIN;

AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; COMPARISON OF MULTIPLE PROTEIN ALIGNMENTS WITH ASSESSMENT OF STATISTICAL SIGNIFICANCE; MATHEMATICAL ANALYSIS; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; SEQUENCE HOMOLOGY; STRUCTURE ACTIVITY RELATION;

EID: 0037423702     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)01371-2     Document Type: Article

References (64)

1. Doolittle R.F. Similar amino acid sequences: chance or common ancestry? Science. 214:1981;149-159.
2. Vogt G., Etzold T., Argos P. An assessment of amino acid exchange matrices in aligning protein sequences: the twilight zone revisited. J. Mol. Biol. 249:1995;816-831.
3. Doolittle R.F. Stein and Moore Award address. Reconstructing history with amino acid sequences. Protein Sci. 1:1992;191-200.
4. Gribskov M., McLachlan A.D., Eisenberg D. Profile analysis: detection of distantly related proteins. Proc. Natl Acad. Sci. USA. 84:1987;4355-4358.
5. Luthy R., Xenarios I., Bucher P. Improving the sensitivity of the sequence profile method. Protein Sci. 3:1994;139-146.
6. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25:1997;3389-3402.
7. Schaffer A.A., Wolf Y.I., Ponting C.P., Koonin E.V., Aravind L., Altschul S.F. IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics. 15:1999;1000-1011.
8. Karplus K., Barrett C., Cline M., Diekhans M., Grate L., Hughey R. Predicting protein structure using only sequence information. Proteins: Struct. Funct. Genet. 37:1999;121-125.
9. Eddy S.R. Profile hidden Markov models. Bioinformatics. 14:1998;755-763.
10. Krogh A., Brown M., Mian I.S., Sjolander K., Haussler D. Hidden Markov models in computational biology. Applications to protein modeling. J. Mol. Biol. 235:1994;1501-1531.
11. Durbin R.E., Krogh A., Mitchison G., Eddy S. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. 1999;Cambridge University Press, Cambridge, UK.
12. Gotoh O. Optimal alignment between groups of sequences and its application to multiple sequence alignment. Comput. Appl. Biosci. 9:1993;361-370.
13. Pietrokovski S. Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucl. Acids Res. 24:1996;3836-3845.
14. Henikoff J.G., Greene E.A., Pietrokovski S., Henikoff S. Increased coverage of protein families with the blocks database servers. Nucl. Acids Res. 28:2000;228-230.
15. Henikoff S., Henikoff J.G., Pietrokovski S. Blocks[plus ]: a non-redundant database of protein alignment blocks derived from multiple compilations. Bioinformatics. 15:1999;471-479.
16. Kunin V., Chan B., Sitbon E., Lithwick G., Pietrokovski S. Consistency analysis of similarity between multiple alignments: prediction of protein function and fold structure from analysis of local sequence motifs. J. Mol. Biol. 307:2001;939-949.
17. Rychlewski L., Jaroszewski L., Li W., Godzik A. Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci. 9:2000;232-241.
18. Yona G., Levitt M. Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J. Mol. Biol. 315:2002;1257-1275.
19. Sunyaev S.R., Eisenhaber F., Rodchenkov I.V., Eisenhaber B., Tumanyan V.G., Kuznetsov E.N. PSIC: profile extraction from sequence alignments with position-specific counts of independent observations. Protein Eng. 12:1999;387-394.
20. Pei J., Grishin N.V. AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics. 17:2001;700-712.
21. Dayhoff M.O., Schwartz R.M., Orcutt B.C. Dayhoff M.O. Atlas of Protein Sequence and Structure. vol. 5:1978;345-352 National Biomedical Research Foundation, Washington, DC.
22. Sjolander K., Karplus K., Brown M., Hughey R., Krogh A., Mian I.S., Haussler D. Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Comput. Appl. Biosci. 12:1996;327-345.
23. Tatusov R.L., Altschul S.F., Koonin E.V. Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks. Proc. Natl Acad. Sci. USA. 91:1994;12091-12095.
24. Eskin E., Grundy W.N., Singer Y. Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences. Bioinformatics. 17:2001;S65-S73.
25. McCullagh P. On the elimination of nuisance parameters in the proportional odds model. J. R. Stat. Soc. B. 46:1984;250-256.
26. Staden R. Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes. Nucl. Acids Res. 12:1984;551-567.
27. Schneider T.D., Stormo G.D., Gold L., Ehrenfeucht A. Information content of binding sites on nucleotide sequences. J. Mol. Biol. 188:1986;415-431.
28. Berg O.G., von Hippel P.H. Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol. 193:1987;723-750.
29. Dodd I.B., Egan J.B. Systematic method for the detection of potential lambda Cro-like DNA-binding regions in proteins. J. Mol. Biol. 194:1987;557-564.
30. Stormo G.D., Hartzell G.W. III. Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl Acad. Sci. USA. 86:1989;1183-1187.
31. Lawrence C.E., Altschul S.F., Boguski M.S., Liu J.S., Neuwald A.F., Wootton J.C. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science. 262:1993;208-214.
32. Henikoff J.G., Henikoff S. Using substitution probabilities to improve position-specific scoring matrices. Comput. Appl. Biosci. 12:1996;135-143.
33. Smith T.F., Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 147:1981;195-197.
34. Gnedenko B. Sur la distribution limite du terme maximum d'une serie aleatoire. Ann. Mathemat. 44:1943;423-453.
35. Gumbel E.J. Statistics of Extremes. 1958;Columbia University Press, New York.
36. Karlin S., Altschul S.F. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci. USA. 87:1990;2264-2268.
37. Karlin S., Dembo A., Kawabata T. Statistical composition of high-scoring segments from molecular sequences. Ann. Stat. 18:1990;571-581.
38. Dembo A., Karlin S. Strong limit theorems of empirical functionals for large exceedances of partial sums of i.i.d. variables. Ann. Probab. 19:1991;1737-1755.
39. Schaffer A.A., Aravind L., Madden T.L., Shavirin S., Spouge J.L., Wolf Y.I., et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucl. Acids Res. 29:2001;2994-3005.
40. Altschul S.F., Bundschuh R., Olsen R., Hwa T. The estimation of statistical parameters for local alignment score distributions. Nucl. Acids Res. 29:2001;351-361.
41. Eddy, S. (1997). Maximum likelihood fitting of extreme value distributions. http://www.genetics.wustl.edu/eddy/publications/ .
42. Altschul S.F., Gish W. Local alignment statistics. Methods Enzymol. 266:1996;460-480.
43. Holm L., Sander C. Touring protein fold space with Dali/FSSP. Nucl. Acids Res. 26:1998;316-319.
44. Dietmann S., Holm L. Identification of homology in protein structure classification. Nature Struct. Biol. 8:2001;953-957.
45. Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:1993;123-138.
46. Sauder J.M., Arthur J.W., Dunbrack R.L. Jr. Large-scale comparison of protein sequence alignment algorithms with structure alignments. Proteins: Struct. Funct. Genet. 40:2000;6-22.
47. Bateman A., et al. The Pfam protein families database. Nucl. Acids Res. 30:2002;276-280.
48. Holm L., Sander C. Mapping the protein universe. Science. 273:1996;595-603.
49. Murzin A.G., Brenner S.E., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:1995;536-540.
50. Lang D., Thoma R., Henn-Sax M., Sterner R., Wilmanns M. Structural evidence for evolution of the beta/alpha barrel scaffold by gene duplication and fusion. Science. 289:2000;1546-1550.
51. Heldin C.H., Miyazono K., ten Dijke P. TGF-beta signalling from cell membrane to nucleus through SMAD proteins. Nature. 390:1997;465-471.
52. Massague J., Wotton D. Transcriptional control by the TGF-beta/Smad signaling system. EMBO J. 19:2000;1745-1754.
53. Moustakas A., Souchelnytskyi S., Heldin C.H. Smad regulation in TGF-beta signal transduction. J. Cell. Sci. 114:2001;4359-4369.
54. Gronostajski R.M. Roles of the NFI/CTF gene family in transcription and development. Gene. 249:2000;31-45.
55. Heger A., Holm L. Picasso: generating a covering set of protein family profiles. Bioinformatics. 17:2001;272-279.
56. Massague J. TGF-beta signal transduction. Annu. Rev. Biochem. 67:1998;753-791.
57. Mermod N., O'Neill E.A., Kelly T.J., Tjian R. The proline-rich transcriptional activator of CTF/NF-I is distinct from the replication and DNA binding domain. Cell. 58:1989;741-753.
58. Gounari F., De Francesco R., Schmitt J., van der Vliet P., Cortese R., Stunnenberg H. Amino-terminal domain of NF1 binds to DNA as a dimer and activates adenovirus DNA replication. EMBO J. 9:1990;559-566.
59. Kim J., Johnson K., Chen H.J., Carroll S., Laughon A. Drosophila Mad binds to DNA and directly mediates activation of vestigial by Decapentaplegic. Nature. 388:1997;304-308.
60. Shi Y., Wang Y.F., Jayaraman L., Yang H., Massague J., Pavletich N.P. Crystal structure of a Smad MH1 domain bound to DNA: insights on DNA binding in TGF-beta signaling. Cell. 94:1998;585-594.
61. Grishin N.V. Mh1 domain of Smad is a degraded homing endonuclease. J. Mol. Biol. 307:2001;31-37.
62. Bandyopadhyay S., Gronostajski R.M. Identification of a conserved oxidation-sensitive cysteine residue in the NFI family of DNA-binding proteins. J. Biol. Chem. 269:1994;29949-29955.
63. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
64. Letunic I., Goodstadt L., Dickens N.J., Doerks T., Schultz J., Mott R., Ciccarelli F., Copley R.R., Ponting C.P., Bork P. Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res. 30:2002;242-244.