Mercurial > repos > peterjc > secreted_protein_workflow

comparison README.rst @ 5:5f3cc8229771 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
4:b14c822a37fe 5:5f3cc8229771
2 secreted proteins from a given protein FASTA file. 2 secreted proteins from a given protein FASTA file.
3 3
4 It runs SignalP v3.0 (Bendtsen et al. 2004) and selects only proteins with a 4 It runs SignalP v3.0 (Bendtsen et al. 2004) and selects only proteins with a
5 strong predicted signal peptide, and then runs TMHMM v2.0 (Krogh et al. 2001) 5 strong predicted signal peptide, and then runs TMHMM v2.0 (Krogh et al. 2001)
6 on those, and selects only proteins without a predicted trans-membrane helix. 6 on those, and selects only proteins without a predicted trans-membrane helix.
7 This workflow was used in Kikuchi et al (2001), and is a simplification of 7 This workflow was used in Kikuchi et al. (2011), and is a simplification of
8 the candidate effector protocol described in Jones et al (2009). 8 the candidate effector protocol described in Jones et al. (2009).
9 9
10 See http://www.galaxyproject.org for information about the Galaxy Project. 10 See http://www.galaxyproject.org for information about the Galaxy Project.
11
12
13 Sample Data
14 ===========
15
16 This workflow was developed and run on several nematode species. For example,
17 try the protein set for Bursaphelenchus xylophilus (Kikuchi et al. 2011):
18
19 ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BUX.v1.2.genedb.protein.fa.gz
20
21 You can upload this directly into Galaxy via this URL. Galaxy will handle
22 removing the gzip compression to give you the FASTA protein file which has
23 18,074 sequences. The expected result (selecting organism type Eukaryote)
24 is a FASTA protein file of 2,297 predicted secreted protein sequences.
11 25
12 26
13 Citation 27 Citation
14 ======== 28 ========
15 29