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Pro-Coffee

Pro-Coffee

Pro-Coffee is a part of the T_Coffee package and implemented for multiple sequence alignment of promoter regions.

Topic

Sequence analysis; DNA; Proteins; RNA

Details

  • Operation: Multiple sequence alignment
  • Input: FASTA
  • Output: ClustalW
  • Software interface: Web user interface
  • Language: C++
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL v3
  • Cost: Free
  • Version name: -
  • Maturity: Stable
  • Credit: -
  • Contact: cedric.notredame _at_ europe.com
  • Collection: T-Coffee

Publications

Erb I, González-Vallinas JR, Bussotti G, Blanco E, Eyras E, Notredame C "Use of ChIP-Seq data for the design of a multiple promoter-alignment method." Nucleic Acids Res. 2012 Apr;40(7):e52. doi: 10.1093/nar/gkr1292. Epub 2012 Jan 9. https://doi.org/10.1093/nar/gkr1292
PMID: 22230796
PMCID: PMC3326335


Notredame C, Higgins DG, Heringa J "T-Coffee: A novel method for fast and accurate multiple sequence alignment." J Mol Biol. 2000 Sep 8;302(1):205-17. https://doi.org/10.1006/jmbi.2000.4042
PMID: 10964570


Magis C, Taly JF, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Notredame C "T-Coffee: Tree-based consistency objective function for alignment evaluation." Methods Mol Biol. 2014;1079:117-29. https://doi.org/10.1007/978-1-62703-646-7_7
PMID: 24170398


Taly JF, Magis C, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Kemena C, Notredame C "Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures." Nat Protoc. 2011 Nov;6(11):1669-82. https://doi.org/10.1038/nprot.2011.393
PMID: 21979275


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