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What are DNA sequence motifs?

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Sequence motifs are becoming increasingly important in the analysis of gene regulation. How do we define sequence motifs, and why should we use sequence logos instead of consensus sequences to represent them? Do they have any relation with binding affinity? How do we search for new instances of a motif in this sea of DNA?

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Figure 1: ROX1 binding sites and sequence motif.

Bob Crimi

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References

  1. Schneider, T.D. & Stephens, R.M. Sequence Logos: a new way to display consensus sequences. Nucleic Acids Res. 18, 6097–6100 (1990).

    Article  CAS  Google Scholar 

  2. Stormo, G.D. DNA binding sites: representation and discovery. Bioinformatics 16, 16–23 (2000).

    Article  CAS  Google Scholar 

  3. Workman, C.T. et al. EnoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res. 33 (Web Server Issue), W389–W392 (2005).

    Article  CAS  Google Scholar 

  4. Matys, V. et al. TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34 suppl. Database issue, D108–D110 (2006).

    Article  CAS  Google Scholar 

  5. Vlieghe, D. et al. A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res. 34 suppl. Database issue, D95–D97 (2006).

    Article  CAS  Google Scholar 

  6. Teixeira, M.C. et al. The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res. 34 suppl. Database issue, D446–451 (2006).

    Article  CAS  Google Scholar 

  7. Zhu, J. & Zhang, M.Q. SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 15, 607–611 (1999).

    Article  CAS  Google Scholar 

  8. Salgado, H. et al. RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res. 34 suppl. Database issue, D394–D397 (2006).

    Article  CAS  Google Scholar 

  9. Munch, R. et al. PRODORIC: prokaryotic database of gene regulation. Nucleic Acids Res. 31, 266–269 (2003).

    Article  CAS  Google Scholar 

  10. Djordjevic, M., Sengupta, A.M. & Shraiman, B.I. A biophysical approach to transcription factor binding site discovery. Genome Res. 13, 2381–2390 (2003).

    Article  CAS  Google Scholar 

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  1. Microbial Systems Division, Biosciences Directorate, Lawrence Livermore National Laboratory, PO Box 808, L-448, Livermore, 94551, California, USA

    Patrik D'haeseleer

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  1. Patrik D'haeseleer
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D'haeseleer, P. What are DNA sequence motifs?. Nat Biotechnol 24, 423–425 (2006). https://doi.org/10.1038/nbt0406-423

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  • DOI: https://doi.org/10.1038/nbt0406-423

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