Comments (6)
RAVEN has functionality to run and parse WoLF PSORT. I've never tried it, and it runs on unix only, but could be useful. Additional predictLocalization function can actually assign localization, trying to reduce the number of transport reactions that need to be added.
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@CarlMalina which database were you using for finding proper localization of enzymes in mitochondria? We could use the same one but for all compartments in the cell
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@BenjaSanchez I have mostly been using MitoMiner (http://mitominer.mrc-mbu.cam.ac.uk/release-4.0/begin.do) which combines experimental evidence for protein localization with GO and UniProt annotation. However, it is quite specific for mitochondrial proteins so I am not sure it is of much use for other compartments.
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I've used PSORTb (http://www.psort.org/) for my reconstruction, and I was pretty happy with the output. However, it is exclusive for prokaryotes but there is https://wolfpsort.hgc.jp/ for eukaryotes.
Not sure how that performs though.
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RAVEN also supports CELLO. It is online-based tool, so you run it online, save the text output in your computer and then use it as input to assign localization. The calculation scores can then be used in predictLocalization. The advantage of CELLO is that it considers multiple criteria when calculating compartment scores (Nearest Neighbour, SVM) rather than relying only on Nearest Neighbour algorithm like PSORT.
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When considering this, take into account that mitochondrial enzymes have been manually curated in mitoYeast-GEM
and will be applied as part of #12.
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Related Issues (20)
- refactor: reduce dependencies modelTests HOT 1
- Feat: A python function for anaerobic condition setup HOT 1
- feat: KEGG pathway annotation
- feat: metSMILES annotation HOT 1
- feat: single ec-code annotation per reaction HOT 5
- feat: Uniprot annotations for all genes HOT 5
- cerevisiae with radiation simulation is possible? HOT 1
- References for anaerobic benchmarking HOT 11
- fix: add missing standard-GEM file
- some memote workflows are failing HOT 3
- Update according to genome update in 2021
- check Lys2 and Leu2 gene associations HOT 1
- Fructose transport is represented as a symporter instead of facilitated diffusion
- reaction references
- duplicate metabolites identified HOT 1
- unable to locate model when running io.read_yeast_model() in Python HOT 1
- Proposed changes to the anaerobic model HOT 2
- feat: function to report if flux vector is ΔG-compatible
- bug:spelling error for r_1024 "enxyme" HOT 2
- reactions r_0533, r_0534, r_0535 appear not balanced HOT 2
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