Genome BioInformatics Research Lab

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    If you use the annotations provided on ABS, please cite:

  • E. Blanco, D. Farré, M. Albà, X. Messeguer and R. Guigó. "ABS: a database
    of Annotated regulatory Binding Sites from orthologous promoters". Nucleic
    Acids Research
    34:D63-D67 (2006). [OPEN ACCESS PUBLICATION]

  • Basic references:

  • 1. B. Lenhard, A. Sandelin, L. Mendoza, P. Engström, N. Jareborg and W.W. Wasserman.
    "Identification of conserved regulatory elements by comparative genome analysis."
    Journal of Biology 2:13 (2003).

  • 2. W. Krivan and W. W. Wasserman
    "A predictive model for regulatory sequences directing liver-specific transcription."
    Genome Research 11:1559-1566 (2001).

  • 3. E.T. Dermitzakis and A.G. Clark
    "Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover."
    Molecular Biology and Evolution 19:1114-1121 (2002).

  • 4. W.W. Wasserman and James W. Fickett
    "Identification of regulatory regions which confer muscle-specific gene expression"
    Journal of Molecular Biology 278: 167-181 (1998) // L.L. Lopez, W.W. Wasserman and J.W. Fickett.
    "Muscle-specific regulation of transcription: a catalog of regulatory elements."

  • 5. M. Blanchette and M. Tompa.
    "Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting."
    Genome Research 12: 739-748 (2002).

  • 6. S.F. Altschul, W. Gish, W. Miller, E.W. Myers and D.J. Lipman.
    "Basic local alignment search tool."
    Journal of Molecular Biology 215: 403-410 (1990).

  • 7. J.D. Thompson, D.G. Higgins and T.J. Gibson.
    "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice."
    Nucleic Acids Research. 22:4673-4680 (1994).

  • 8. N. Bray, I. Dubchak and L. Pachter.
    "AVID: A Global Alignment Program"
    Genome Research 13:97-102 (2003).

  • 9. M. Brudno, C. Do, G. Cooper, M.F. Kim, E. Davydov, E.D. Green, A. Sidow and S. Batzoglou.
    "LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA"
    Genome Research 13:721-731 (2003).

  • 10. P. Rice, I. Longden and A. Bleasby.
    "EMBOSS: The European Molecular Biology Open Software Suite."
    Trends in Genetics 16, 6:276-277 (2000).

  • 11. J.F. Abril and R. Guigo.
    "gff2ps: visualizing genomic annotations."
    Bioinformatics, 16, 743-744 (2000).

  • 12. G.E. Crooks, G. Hon, J.M. Chandonia, S.E. Brenner.
    "WebLogo: A sequence logo generator"
    Genome Research, 14:1188-1190, (2004).

  • 13. E. Blanco, X. Messeguer and R. Guigó.
    "Novel computational methods to characterize regulatory regions."
    CSHL - Systems Biology (Poster), New York, USA (2004)


The current version of ABS home page has been written by Enrique Blanco
Thanks to J.F. Abril and O. Gonzalez for technical support.
Thanks to M. Pignatelli for web testing.

CopyRight © 2005

ABS is under GNU General Public License.

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