Mercurial > repos > peterjc > venn_list
view README.txt @ 1:f1323a651777 draft
Uploaded fix to stray space in dependencies
| author | peterjc |
|---|---|
| date | Mon, 06 May 2013 14:04:34 -0400 |
| parents | |
| children |
line wrap: on
line source
This Tool Shed Repository contains a workflow for comparing three RXLR prediction methods with a Venn Diagram, and creates a FASTA file of any proteins passing all three methods. References ========== Stephen C. Whisson, Petra C. Boevink, Lucy Moleleki, Anna O. Avrova, Juan G. Morales, Eleanor M. Gilroy, Miles R. Armstrong, Severine Grouffaud, Pieter van West, Sean Chapman, Ingo Hein, Ian K. Toth, Leighton Pritchard and Paul R. J. Birch A translocation signal for delivery of oomycete effector proteins into host plant cells. Nature 450:115-118, 2007. http://dx.doi.org/10.1038/nature06203 Joe Win, William Morgan, Jorunn Bos, Ksenia V. Krasileva, Liliana M. Cano, Angela Chaparro-Garcia, Randa Ammar, Brian J. Staskawicz and Sophien Kamoun. Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes. The Plant Cell 19:2349-2369, 2007. http://dx.doi.org/10.1105/tpc.107.051037 Souvik Bhattacharjee, N. Luisa Hiller, Konstantinos Liolios, Joe Win, Thirumala-Devi Kanneganti, Carolyn Young, Sophien Kamoun and Kasturi Haldar. The malarial host-targeting signal is conserved in the Irish potato famine pathogen. PLoS Pathogens, 2(5):e50, 2006. http://dx.doi.org/10.1371/journal.ppat.0020050 Availability ============ This workflow is available on the main Galaxy Tool Shed: http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow Development is being done on github here: https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow Dependencies ============ These dependencies should be resolved automatically via the Galaxy Tool Shed: * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id * http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list However, at the time of writing those Galaxy tools have their own dependencies required for this workflow which require manual installation (SignalP v3.0, HMMER v2.0, and the R/Bioconductor package limma).