If you use CPG or RNAit in a publication, please cite as follows:

Field, H.I., Coulson, R.M.R., and Field, M.C., (2013) ‘An automated graphics tool for comparative genomics: The Coulson plot generator.’ BMC Bioinformatics 14 141 [PDF]

Redmond, S., Vadivelu, J., and Field, M.C., (2003) ‘RNAit: An automated web-based tool for the selection of RNAi targets in Trypanosoma brucei.’ Molecular and Biochemical Parasitology 128 115 - 118 [PDF]


The Coulson plot is featured in the following publications and many more:
Field, M.C., Gabernet-Castello, C., and Dacks, JB., (2007) 'Reconstructing the evolution of the endocytic system: insights from genomics and molecular cell biology.’ Advances in Experimental Medicine and Biology 607 84-962.

Koumandou, V.L., Dacks, J.B., Coulson, R.M.R., and Field, M.C., (2007) ‘Control systems for membrane fusion in the ancestral eukaryote; evolution of tethering complexes and SM proteins.’ BMC Evolutionary Biology 7 29.

Leung, K-F., Dacks, J.D., and Field, M.C., (2008) ‘Evolution of the multi-vesicular body ESCRT machinery; subunit retention and functional equivalence across the eukaryotic lineage.’ Traffic 9 1698-716.

Nevin, W.D., and Dacks, J.B., (2009) ‘Repeated secondary loss of adaptin complex genes in the Apicomplexa.’ Parasitology International 58 86-94.

Dokudovskaya, S., Waharte, F., Schlessinger, A., Pieper, U., Devos, D., Cristea, I.M., Williams, R., Salamero, J., Chait, B.T., Sali, A., Field, M.C., Rout, M.P., and Dargemont, C., (2011) 'A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae.' Molecular and Cellular Proteomics 10 M110.006478.

Herman, E.K., Walker, G., van der Giezen, M., and Dacks, J.B., (2011) ‘Multi-vesicular bodies in the enigmatic amoeboflagellate Breviata anathema and the evolution of ESCRT 0.’ Journal of Cell Science 2011 124 613-21.

Hirst, J.D.B.L, Francisco, G.C., Sahlender, D.A., Seaman, M.N., Dacks, J.B., and Robinson, M.S., (2011) ‘The fifth adaptor protein complex.’ PLoS Biology 9 e1001170.

Klute, M.J., Melancon, P., and Dacks, J.B., (2011) ‘Evolution and diversity of the Golgi.’ Cold Spring Harbor Perspectives in Biology 3 a007849.

Koumandou, V.L., Dacks, J.B., and Field, M.C., (2011) ‘Evolutionary reconstruction of the retromer complex and its function in Trypanosoma brucei.’ Journal of Cell Science 124 1496 - 1509.

Manna, P., Kelly, S., and Field, M.C., (2013) ‘Co-evolution of antigenic variation and adaptins in trypanosomatids.’ Molecular and Protein Evolution 67 123 - 128

Schlacht, A., Mowbrey, K., Elias, M., Kahn, R.A., and Dacks, J.B., (2013) 'Ancient complexity, opisthokont plasticity and discovery of the 11th subfamily of Arf-GAP proteins.' Traffic 14 639 - 649

Field, H.I., Coulson, R.M.R., and Field, M.C., (2013) ‘An automated graphics tool for comparative genomics: The Coulson plot generator.’ BMC Bioinformatics 14 141.

vanDam, T.P.J., Townsend, M.J, Turk, M., Schlessinger, A., Sali, A., Field, M.C., and Huynen, M., (2013) ‘Evolution of modular intraflagellar transport from a coatomer-like progenitor.’ Proceedings of the National Academy of Science (USA) 110 6943 - 6948.

Wideman, J.G., Gawryluk, R.M., Gray, M.W., and Dacks, J.B., (2013) ‘The ancient and widespread nature of the ER-mitochondria encounter structure.’ Molecular Biology and Evolution 30 2044-9.

Spycher, C., Herman, E.K., Morf, L., Qi, W., Rehrauer, H., Aquino Fournier, C., Dacks, J.B., and Hehl, A.B. (2013) ‘An ER-directed transcriptional response to unfolded protein stress in the absence of conserved sensor-transducer proteins in Giardia lamblia.’ Mol Microbiol. 88 754-71.

Klinger, C.M., Klute, M.J., and Dacks, J.B.(2013) ‘Comparative genomic analysis of multi-subunit tethering complexes demonstrates an ancient pan-eukaryotic complement and sculpting in Apicomplexa.’ PLoS One 8 e76278.

Schlacht, A., Emily K. Herman, E.K., Klute, M.J., Field, M.C., and Dacks, J.B., (2014) ‘Missing pieces of an ancient puzzle: evolution of the membrane-trafficking system.’ In “Origin And Evolution Of Eukaryotes’, Keeling, P.J. and Koonin, E.V., eds., Cold Spring Harbor Laboratory Press, ISBN-13: 9781621820284.

 

The Coulson plot generator (CPG) is an open source Java application for creating a multiple pie diagram and comparing subunit occupancy across a range of entities as shown at left. Numbers of pies, segments, labels and colors are customizable. CPG creates an editable PDF from a comma separated text file (.csv), and has zoom capability for larger datasets. The format is especially useful for visualizing patterns in big data. Originally developed for comparative genomics, the Coulson plot is also appropriate for display of other hierarchical data. The format was invented by Richard M. Coulson and coded as an application by Helen I. Field. The icon was designed by MCF.

CPG available as binary or source code at GitHub. Download: MacOS | WinLin

RNAit is a web-based tool for the identification of primers for RNAi in kinetoplastids. The software uses Primer3 to predict suitable primers for PCR, and then checks that the predicted product has no off-target potential. Data are returned for the user to assess, settings are customizable. RNAit was originally developed by Seth Redmond and the present iteration has been recoded by James Abbott of the Barton group and runs with a python backend within a virtual machine; your data are completely secure. An updated version for CRISPR gRNA design is under development. Comments and suggestions welcome.

RNAit source code is available at GitHub and here. Web interface here. (coming soon)