Advertisement

Pyicos: A Flexible Tool Library for Analyzing Protein-Nucleotide Interactions with Mapped Reads from Deep Sequencing

  • Juan González-Vallinas
  • Sonja Althammer
  • Eduardo Eyras
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6620)

Abstract

Deep DNA or RNA sequencing and posterior mapping to a reference sequence is becoming a standard procedure in molecular biology research. Analyzing millions of mapped reads is a challenging task that doesn’t have a unique solution, because experiments using deep sequencing technology vary a great deal among each other. This is why we have developed a flexible tool library called Pyicos, which aims to help biologists in their research when performing their analysis on mapped reads.

Keywords

Deep sequencing High-throughput sequencing ChIP-Seq CLIP-Seq transcription factor genomics DNA RNA Peak Calling software development 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Bennett, S.: Solexa Ltd. Pharmacogenomics 5(4), 433–438 (2004)CrossRefGoogle Scholar
  2. 2.
    Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., Zeng, T., et al.: Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4(8), 651–657 (2007)CrossRefGoogle Scholar
  3. 3.
    Schones, D.E., Cui, K., Cuddapah, S., Roh, T., Barski, A., Wang, Z., et al.: Dynamic regulation of nucleosome positioning in the human genome. Cell 132(5), 887–898 (2008)CrossRefGoogle Scholar
  4. 4.
    Sanford, J.R., Wang, X., Mort, M., Vanduyn, N., Cooper, D.N., Mooney, S.D., et al.: Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res. 19(3), 381–394 (2009)CrossRefGoogle Scholar
  5. 5.
    Trapnell, C., Salzberg, S.L.: How to map billions of short reads onto genomes. Nat. Biotechnol. 27(5), 455–457 (2009)CrossRefGoogle Scholar
  6. 6.
    Li, H., Ruan, J., Durbin, R.: Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 18(11), 1851–1858 (2008)CrossRefGoogle Scholar
  7. 7.
    Li, R., Li, Y., Kristiansen, K., Wang, J.: SOAP: short oligonucleotide alignment program. Bioinformatics 24(5), 713–714 (2008)CrossRefGoogle Scholar
  8. 8.
    Fejes, A.P., Robertson, G., Bilenky, M., Varhol, R., Bainbridge, M., Jones, S.J.M.: FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 24(15), 1729–1730 (2008)CrossRefGoogle Scholar
  9. 9.
    Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., et al.: Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9(9), R137 (2008)CrossRefGoogle Scholar
  10. 10.
    Kharchenko, P.V., Tolstorukov, M.Y., Park, P.: Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat. Biotechnol. 26(12), 1351–1359 (2008)CrossRefGoogle Scholar
  11. 11.
    Pepke, S., Wold, B., Mortazavi, A.: Computation for ChIP-seq and RNA-seq studies. Nat. Meth. 6(11s), S22–S32 (2009)CrossRefGoogle Scholar
  12. 12.
    Gottardo, R.: Modeling and Analysis of ChIP-Chip Experiments (Internet). In: Chromatin Immunoprecipitation Assays, pp. 133–143 (2009), http://dx.doi.org/10.1007/978-1-60327-414-2_9
  13. 13.
    Yeo, G.W., Coufal, N.G., Liang, T.Y., Peng, G.E., Fu, X., Gage, F.: An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat. Struct. Mol. Biol. 16(2), 130–137 (2009)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Juan González-Vallinas
    • 1
  • Sonja Althammer
    • 1
  • Eduardo Eyras
    • 1
    • 2
  1. 1.Computational Genomics GroupUniversitat Pompeu Fabra, PRBBBarcelonaSpain
  2. 2.Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain

Personalised recommendations