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A Faster Algorithm for Motif Finding in Sequences from ChIP-Seq Data

  • Federico Zambelli
  • Giulio Pavesi
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7548)

Abstract

Motif finding in nucleotide sequences for the discovery of over–represented transcription factor binding sites is a very challenging problem, both from the computational and the experimental points of view. Transcription factors in fact recognize very weakly conserved sequence elements, that in typical applications are very hard to discriminate against random sequence similarities. Recent advances in technology like ChIP-Seq can generate better datasets to be investigated, in which the degree of conservation of binding sites is higher: on the other hand, the size itself of the datasets has posed new challenges for the design of efficient algorithms able to produce results in reasonable time. In this work we present an updated version of our algorithm Weeder, in which time and space requirements are significantly reduced and, moreover, also the accuracy of the results is notably improved.

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References

  1. 1.
    Lemon, B., Tjian, R.: Orchestrated response: a symphony of transcription factors for gene control. Genes. Dev. 14, 2551–2569 (2000)CrossRefGoogle Scholar
  2. 2.
    Stormo, G.D.: DNA binding sites: representation and discovery. Bioinformatics 16, 16–23 (2000)CrossRefGoogle Scholar
  3. 3.
    Pavesi, G., Mauri, G., Pesole, G.: In silico representation and discovery of transcription factor binding sites. Brief Bioinform. 5, 217–236 (2004)CrossRefGoogle Scholar
  4. 4.
    Collas, P., Dahl, J.A.: Chop it, ChIP it, check it: the current status of chromatin immunoprecipitation. Front Biosci. 13, 929–943 (2008)CrossRefGoogle Scholar
  5. 5.
    Mardis, E.R.: ChIP-seq: welcome to the new frontier. Nat. Methods 4, 613–614 (2007)CrossRefGoogle Scholar
  6. 6.
    Pavesi, G.: Motif finding from Chips to ChIPs. In: Elnitski, L., Piontkivska, H., Welch, L.R. (eds.) Advances in Genomic Sequence Analysis and Pattern Discovery. World Scientific Publishing Co. (2011)Google Scholar
  7. 7.
    Mercier, E., Droit, A., Li, L., Robertson, G., Zhang, X., Gottardo, R.: An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq. PLoS One 6, e16432 (2011)Google Scholar
  8. 8.
    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., Makeev, V.J., Mironov, A.A., Noble, W.S., Pavesi, G., Pesole, G., Rgnier, M., Simonis, N., Sinha, S., Thijs, G., van Helden, J., Vandenbogaert, M., Weng, Z., Workman, C., Ye, C., Zhu, Z.: Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol. 23, 137–144 (2005)CrossRefGoogle Scholar
  9. 9.
    Sagot, M.-F.: Spelling Approximate Repeated or Common Motifs Using a Suffix Tree. In: Lucchesi, C.L., Moura, A.V. (eds.) LATIN 1998. LNCS, vol. 1380, pp. 111–127. Springer, Heidelberg (1998)Google Scholar
  10. 10.
    Pavesi, G., Mereghetti, P., Mauri, G., Pesole, G.: Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Res. 32, W199–W203 (2004)CrossRefGoogle Scholar
  11. 11.
    Ettwiller, L., Paten, B., Ramialison, M., Birney, E., Wittbrodt, J.: Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation. Nat. Methods 4, 563–565 (2007)CrossRefGoogle Scholar
  12. 12.
    Linhart, C., Halperin, Y., Shamir, R.: Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets. Genome Res. 18, 1180–1189 (2008)CrossRefGoogle Scholar
  13. 13.
    Zhang, Y., Waterman, M.S.: DNA sequence assembly and multiple sequence alignment by an Eulerian path approach. In: Cold Spring Harb. Symp. Quant. Biol., vol. 68, pp. 205–212 (2003)Google Scholar
  14. 14.
    Zerbino, D.R., Birney, E.: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829 (2008)CrossRefGoogle Scholar
  15. 15.
    Martianov, I., Choukrallah, M.A., Krebs, A., Ye, T., Legras, S., Rijkers, E., Van Ijcken, W., Jost, B., Sassone-Corsi, P., Davidson, I.: Cell-specific occupancy of an extended repertoire of CREM and CREB binding loci in male germ cells. BMC Genomics 11, 530 (2010)CrossRefGoogle Scholar
  16. 16.
    Bailey, T.L.: DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics 27, 1653–1659 (2011)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Federico Zambelli
    • 1
  • Giulio Pavesi
    • 1
  1. 1.Dept. of Biomolecular Science and BiotechnologyUniversity of MilanMilanItaly

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