Expresso

Expresso is a software tool to identify transcription factor binding sites in plants using ChIP-Seq data sets. The Expresso algorithm constructs multiple sequence alignments based on structural information from PDB database.

Topic

ChIP-seq;Transcription factors and regulatory sites;Gene regulation

Detail

  • Operation: Transcription factor binding site prediction;Expression analysis

  • Software interface: Web user interface

  • Language: PHP;Python;Shell

  • License: The MIT licence

  • Cost: Free

  • Version name: 2.0

  • Credit: CNRS (Centre National de la Recherche Scientifique), Sanofi-Aventis Pharma SA., Marseille–Nice Génopole and the French National Genomic Network (RNG).

  • Input: -

  • Output: -

  • Contact: delasa@vt.edu, kvel@vt.edu, Cedric Notredame cedric.notredame@europe.com

  • Collection: -

  • Maturity: Mature

Publications

  • Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee.
  • Armougom F, Moretti S, Poirot O, Audic S, Dumas P, Schaeli B, Keduas V, Notredame C. Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W604-8. doi: 10.1093/nar/gkl092. PMID: 16845081; PMCID: PMC1538866.
  • https://doi.org/10.1093/nar/gkl092
  • PMID: 16845081
  • PMC: PMC1538866

Download and documentation

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