Pattern discovery and pattern matching in non-coding sequences

Web sites

Regulatory Sequence Analysis tools

• temporary local site (for the hands-on): http://bioicrs1.chem.uva.nl/rsa-tools/
• permanent site: http://www.ucmb.ulb.ac.be/bioinformatics/rsa-tools/

Sample families

• Known regulons
• Gene clusters from DNA chip experiments
• Random sequences

Suggested readings

String-based approaches

• van Helden J, Rios AF, Collado-Vides J. Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res. 2000 Apr 15;28(8):1808-1818. PMID:10734201
  
• van Helden, J., André, B., and Collado-Vides, J. (1998). Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol.Biol. 281:827-842.
• van Helden, J., André, B., and Collado-Vides, J. (1999).A web site for the computational analysis of yeast regulatory sequences. Yeast, in press.
• van Helden, J. , del Olmo, M., and Pérez-Ortín, J.E.Genomic computational analysis of yeast downstream sequences reveals putative polyadenylation efficiency elements. submitted.
• van Helden, J., Rios, A., Collado-Vides, J. Extracting cis-acting regulatory elements from yeast non-coding sequences by analysis of spaced dyads. in prep

Gibbs sampling

• Hughes JD, Estep PW, Tavazoie S, Church GM. Computational identification of cis-regulatory elements associated with groups of functionally related genes in saccharomyces cerevisiae. J Mol Biol. 2000 Mar 10;296(5):1205-14. PMID: 10698627; UI: 20198293 PMID:10698627
  
• Roth FP, Hughes JD, Estep PW, Church GM. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol. 1998 Oct;16(10):939-45. PMID: 9788350; UI: 99002399
  
• Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM. Systematic determination of genetic network architecture. Nat Genet. 1999 Jul;22(3):281-5. PMID: 10391217; UI: 99318101
  
• Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science. 1993 Oct 8;262(5131):208-14. PMID: 8211139; UI: 94023958
  Comment: first application of the gibbs sampler to discover motifs in protein sequences