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Commit message:
Uploaded v0.0.1e with links to sample data in README |
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modified:
README.rst |
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| diff -r b14c822a37fe -r 5f3cc8229771 README.rst --- a/README.rst Mon Aug 19 11:38:03 2013 -0400 +++ b/README.rst Tue Aug 20 07:37:19 2013 -0400 |
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| @@ -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 ======== |