The twilight zone of cis element alignments

Nucleic Acids Research

Volumn 41, Issue 3, 2013, Pages 1438-1449

  Sebastian, Alvaro ^a   Contreras Moreira, Bruno ^a,b  

^a CSIC   (Spain)

^b FUNDACIÓN ARAID   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; CONTROLLED STUDY; DNA CONFORMATION; DNA PROTEIN COMPLEX; PRIORITY JOURNAL; PROTEIN CONFORMATION; REGULATORY DNA SEQUENCE; REGULATORY SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

BINDING SITES; DNA; NUCLEOTIDE MOTIFS; POSITION-SPECIFIC SCORING MATRICES; REGULATORY ELEMENTS, TRANSCRIPTIONAL; SEQUENCE ALIGNMENT; TRANSCRIPTION FACTORS;

EID: 84873675713     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1301     Document Type: Article

References (48)

1. Stormo,G.D. (2000) DNA binding sites: representation and discovery. Bioinformatics, 16, 16-23.
2. Garner,M.M. and Revzin,A. (1981) A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res., 9, 3047-3060.
3. O'Neill,L.P. and Turner,B.M. (1996) Immunoprecipitation of chromatin. Methods Enzymol., 274, 189-197.
4. Galas,D.J. and Schmitz,A. (1978) DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res., 5, 3157-3170.
5. Ren,B., Robert,F., Wyrick,J.J., Aparicio,O., Jennings,E.G., Simon,I., Zeitlinger,J., Schreiber,J., Hannett,N., Kanin,E. et al. (2000) Genome-wide location and function of DNA binding proteins. Science, 290, 2306-2309.
6. Johnson,D.S., Mortazavi,A., Myers,R.M. and Wold,B. (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science, 316, 1497-1502.
7. Berger,M.F. and Bulyk,M.L. (2009) Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat. Protoc., 4, 393-411.
8. Stormo,G.D. and Hartzell,G.W.,3rd. (1989) Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl Acad. Sci. USA, 86, 1183-1187.
9. Bailey,T.L., Williams,N., Misleh,C. and Li,W.W. (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res., 34, W369-W373.
10. Tompa M., Li,N., Bailey,T.L., Church,G.M., De Moor,B., Eskin,E., Favorov,A.V., Frith,M.C., Fu,Y., Kent,W.J. et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol., 23, 137-144.
11. Frith,M.C., Hansen,U., Spouge,J.L. and Weng,Z. (2004) Finding functional sequence elements by multiple local alignment. Nucleic Acids Res., 32, 189-200.
12. Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
13. Matys,V., Fricke,E., Geffers,R., Gossling,E., Haubrock,M., Hehl,R., Hornischer,K., Karas,D., Kel,A.E., Kel-Margoulis,O.V. et al. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
14. Bryne,J.C., Valen,E., Tang,M.H., Marstrand,T., Winther,O., da Piedade,I., Krogh,A., Lenhard,B. and Sandelin,A. (2008) JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res., 36, D102-106.
15. Gama-Castro,S., Jimenez-Jacinto,V., Peralta-Gil,M., Santos-Zavaleta,A., Penaloza-Spinola,M.I., Contreras-Moreira,B., Segura-Salazar,J., Muniz-Rascado,L., Martinez-Flores,I., Salgado,H. et al. (2008) RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res., 36, D120-D124.
16. Morozov,A.V., Havranek,J.J., Baker,D. and Siggia,E.D. (2005) Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res., 33, 5781-5798.
17. Contreras-Moreira,B. and Collado-Vides,J. (2006) Comparative footprinting of DNA-binding proteins. Bioinformatics, 22, e74-e80.
18. Contreras-Moreira,B. (2010) 3D-footprint: a database for the structural analysis of protein-DNA complexes. Nucleic Acids Res., 38, D91-D97.
19. Alamanova,D., Stegmaier,P. and Kel,A. (2010) Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies. BMC Bioinformatics, 11, 225.
20. Angarica,V.E., Perez,A.G., Vasconcelos,A.T., Collado-Vides,J. and Contreras-Moreira,B. (2008) Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics, 9, 436.
21. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
22. Mahony,S., Auron,P.E. and Benos,P.V. (2007) DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. PLoS Comput. Biol., 3, e61.
23. Frith,M.C., Fu,Y., Yu,L., Chen,J.F., Hansen,U. and Weng,Z. (2004) Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res., 32, 1372-1381.
24. Turatsinze,J.V., Thomas-Chollier,M., Defrance,M. and van Helden,J. (2008) Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat. Protoc., 3, 1578-1588.
25. Bailey,T.L. and Gribskov,M. (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics, 14, 48-54.
26. Chen,Q.K., Hertz,G.Z. and Stormo,G.D. (1995) MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices. Comput. Appl. Biosci., 11, 563-566.
27. Sander,C. and Schneider,R. (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins, 9, 56-68.
28. Rost,B. (1999) Twilight zone of protein sequence alignments. Protein Eng., 12, 85-94.
29. Keich,U. and Pevzner,P.A. (2002) Finding motifs in the twilight zone. Bioinformatics, 18, 1374-1381.
30. Newburger,D.E. and Bulyk,M.L. (2009) UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res., 37, D77-D82.
31. Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
32. Finn,R.D., Mistry,J., Tate,J., Coggill,P., Heger,A., Pollington,J.E., Gavin,O.L., Gunasekaran,P., Ceric,G., Forslund,K. et al. (2010) The Pfam protein families database. Nucleic Acids Res., 38, D211-D222.
33. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
34. Li,W. and Godzik,A. (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658-1659.
35. Ortiz,A.R., Strauss,C.E. and Olmea,O. (2002) MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci., 11, 2606-2621.
36. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
37. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
38. Mahony,S. and Benos,P.V. (2007) STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res., 35, W253-W258.
39. R Development Core Team. (2009) R Foundation for Statistical Computing. Austria, Vienna.
40. Green,D.M. and Swets,J.A. (1966) Signal Detection Theory and Psychophysics. New York, Wiley.
41. Sonego,P., Kocsor,A. and Pongor,S. (2008) ROC analysis: applications to the classification of biological sequences and 3D structures. Brief Bioinform., 9, 198-209.
42. Sing,T., Sander,O., Beerenwinkel,N. and Lengauer,T. (2005) ROCR: visualizing classifier performance in R. Bioinformatics, 21, 3940-3941.
43. Thomas-Chollier,M., Sand,O., Turatsinze,J.V., Janky,R., Defrance,M., Vervisch,E., Brohee,S. and van Helden,J. (2008) RSAT: regulatory sequence analysis tools. Nucleic Acids Res., 36, W119-W127.
44. Noyes,M.B., Christensen,R.G., Wakabayashi,A., Stormo,G.D., Brodsky,M.H. and Wolfe,S.A. (2008) Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell, 133, 1277-1289.
45. Berger,M.F., Badis,G., Gehrke,A.R., Talukder,S., Philippakis,A.A., Pena-Castillo,L., Alleyne,T.M., Mnaimneh,S., Botvinnik,O.B., Chan,E.T. et al. (2008) Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell, 133, 1266-1276.
46. Raviscioni,M., Gu,P., Sattar,M., Cooney,A.J. and Lichtarge,O. (2005) Correlated evolutionary pressure at interacting transcription factors and DNA response elements can guide the rational engineering of DNA binding specificity. J. Mol. Biol., 350, 402-415.
47. Siggers,T.W., Silkov,A. and Honig,B. (2005) Structural alignment of protein-DNA interfaces: insights into the determinants of binding specificity. J. Mol. Biol., 345, 1027-1045.
48. Claverie,J.M. and Audic,S. (1996) The statistical significance of nucleotide position-weight matrix matches. Comput. Appl. Biosci., 12, 431-439.