Methods for Discovery and Characterization of DNA Sequence Motifs - Bioinformatics: A Swiss Perspective - page 31

26. Xie X, Mikkelsen TS, Gnirke A et al . (2007) Systematic discovery of regulatory
motifs in conserved regions of the human genome, including thousands of
CTCF insulator sites. Proc Natl Acad Sci USA 104 (17): 7145-50.
27. Coward E. (1999) Shufflet: shuffling sequences while conserving the k -let
counts. Bioinformatics 15 (12): 1058-9.
28. Copley RR, Ponting CP, Schultz J, Bork P. (2002) Sequence analysis of mul-
tidomain proteins: past perspectives and future directions. Adv Protein Chem
61 : 75-98.
29. Hu J, Li B, Kihara D. (2005) Limitations and potentials of current motif
discovery algorithms. Nucleic Acids Res 33 (15): 4899-913.
30. Tompa M, Li N, Bailey TL et al . (2005) Assessing computational tools for the
discovery of transcription factor binding sites. Nat Biotechnol 23 (1): 137-44.
31. Wingender E. (2008) The TRANSFAC project as an example of framework
technology that supports the analysis of genomic regulation. Brief Bioinform
9 (4): 326-32.
32. Gama-Castro S, Jiménez-Jacinto V, Peralta-Gil M et al . (2008) RegulonDB
(version 6.0): gene regulation model of Escherichia coli K-12 beyond transcrip-
tion, active (experimental) annotated promoters and Textpresso navigation.
Nucleic Acids Res 36 (Database issue): D120-4.
33. Bucher P, Bryan B. (1984) Signal search analysis: a new method to localize and
characterize functionally important DNA sequences. Nucleic Acids Res 12 (1 Pt 1):
287-305.
34. Bucher P. (1990) Weight matrix descriptions of four eukaryotic RNA poly-
merase II promoter elements derived from 502 unrelated promoter sequences.
J Mol Biol 212 (4): 563-78.
35. Bucher P, Trifonov EN. (1986) Compilation and analysis of eukaryotic POL II
promoter sequences. Nucleic Acids Res 14 (24): 10009-26.
36. Schmid CD, Perier R, Praz V, Bucher P. (2006) EPD in its twentieth year:
towards complete promoter coverage of selected model organisms. Nucleic Acids
Res 34 (Database issue): D82-5.
37. Roulet E, Busso S, Camargo AA et al . (2002) High-throughput SELEX-SAGE
method for quantitative modeling of transcription-factor binding sites. Nat
Biotechnol 20 (8): 831-5.
38. Wakaguri H, Yamashita R, Suzuki Y et al . (2008) DBTSS: database of transcription
start sites, progress report 2008. Nucleic Acids Res 36 (Database issue): D97-101.
39. Kawaji H, Kasukawa T, Fukuda S et al . (2006) CAGE Basic/Analysis Databases:
the CAGE resource for comprehensive promoter analysis. Nucleic Acids Res
34 (Database issue): D632-6.
40. Roth FP, Hughes JD, Estep PW, Church GM. (1998) Finding DNA regulatory
motifs within unaligned noncoding sequences clustered by whole-genome
mRNA quantitation. Nat Biotechnol 16 (10): 939-45.