Mercurial > repos > peterjc > secreted_protein_workflow

changeset 5:5f3cc8229771 draft

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Uploaded v0.0.1e with links to sample data in README
author peterjc
date Tue, 20 Aug 2013 07:37:19 -0400
parents b14c822a37fe
children 36b2c2b5051e
files README.rst
diffstat 1 files changed, 16 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/README.rst	Mon Aug 19 11:38:03 2013 -0400
+++ b/README.rst	Tue Aug 20 07:37:19 2013 -0400
@@ -4,12 +4,26 @@
 It runs SignalP v3.0 (Bendtsen et al. 2004) and selects only proteins with a
 strong predicted signal peptide, and then runs TMHMM v2.0 (Krogh et al. 2001)
 on those, and selects only proteins without a predicted trans-membrane helix.
-This workflow was used in Kikuchi et al (2001), and is a simplification of
-the candidate effector protocol described in Jones et al (2009).
+This workflow was used in Kikuchi et al. (2011), and is a simplification of
+the candidate effector protocol described in Jones et al. (2009).
 
 See http://www.galaxyproject.org for information about the Galaxy Project.
 
 
+Sample Data
+===========
+
+This workflow was developed and run on several nematode species. For example,
+try the protein set for Bursaphelenchus xylophilus (Kikuchi et al. 2011):
+
+ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BUX.v1.2.genedb.protein.fa.gz
+
+You can upload this directly into Galaxy via this URL. Galaxy will handle
+removing the gzip compression to give you the FASTA protein file which has
+18,074 sequences. The expected result (selecting organism type Eukaryote)
+is a FASTA protein file of 2,297 predicted secreted protein sequences.
+
+
 Citation
 ========