Pro-Coffee is a part of the T_Coffee package and implemented for multiple sequence alignment of promoter regions.
Sequence analysis; DNA; Proteins; RNA
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
If you find errors, please report here.
SECTIONS
TutorialsFind thousands of Bioinformatics and Life Science software tools and databases in the newly launched
Ads