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What it does

This calls the WoLF PSORT tool for prediction of eukaryote protein subcellular localization.

The input is a FASTA file of protein sequences, and the output is tabular with four columns (multiple rows per protein):

Column	Description
1	Sequence identifier
2	Compartment
3	Score
4	Prediction rank

Localization Compartments

The table below gives the WoLF PSORT localization site definitions, and the corresponding Gene Ontology (GO) term.

Abbrev	Localization Site	GO Cellular Component
chlo	chloroplast	0009507, 0009543
cyto	cytosol	0005829
cysk	cytoskeleton	0005856(2)
E.R.	endoplasmic reticulum	0005783
extr	extracellular	0005576, 0005618
golg	Golgi apparatus	0005794(1)
lyso	lysosome	0005764
mito	mitochondria	0005739
nucl	nuclear	0005634
pero	peroxisome	0005777(2)
plas	plasma membrane	0005886
vacu	vacuolar membrane	0005774(2)

Numbers in parentheses, such as "0005856(2)" indicate that descendant "part_of" cellular components were also included, up to the specified depth (2 in this case). For example, all of the children and grandchildren of "GO:0005856" were included as "cysk".

Additionally compound predictions like mito_nucl are also given.

Notes

The raw output from WoLF PSORT looks like this (space separated), showing two proteins:

gi\|301087619\|ref\|XP_002894699.1\|	extr 12, mito 4, E.R. 3, golg 3, mito_nucl 3
gi\|301087623\|ref\|XP_002894700.1\|	extr 21, mito 2, cyto 2, cyto_mito 2

This is reformatted into a tabular file as follows for use in Galaxy:

#ID	Compartment	Score	Rank
gi\|301087619\|ref\|XP_002894699.1\|	extr	12	1
gi\|301087619\|ref\|XP_002894699.1\|	mito	4	2
gi\|301087619\|ref\|XP_002894699.1\|	E.R.	3	3
gi\|301087619\|ref\|XP_002894699.1\|	golg	3	4
gi\|301087619\|ref\|XP_002894699.1\|	mito_nucl	3	5
gi\|301087623\|ref\|XP_002894700.1\|	extr	21	1
gi\|301087623\|ref\|XP_002894700.1\|	mito	2	2
gi\|301087623\|ref\|XP_002894700.1\|	cyto	2	3
gi\|301087623\|ref\|XP_002894700.1\|	cyto_mito	2	4

This way you can easily filter for things like having a top prediction for mitochondria (c2=='mito' and c4==1), or extracellular with a score of at least 10 (c2=='extr' and 10<=c3), and so on.

References

If you use this Galaxy tool in work leading to a scientific publication please cite the following papers:

Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PeerJ 1:e167 https://doi.org/10.7717/peerj.167

Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, and Kenta Nakai (2007). WoLF PSORT: Protein Localization Predictor. Nucleic Acids Research, 35(S2), W585-W587. https://doi.org/10.1093/nar/gkm259

Paul Horton, Keun-Joon Park, Takeshi Obayashi and Kenta Nakai (2006). Protein Subcellular Localization Prediction with WoLF PSORT. Proceedings of the 4th Annual Asia Pacific Bioinformatics Conference APBC06, Taipei, Taiwan. pp. 39-48.