Prediction of Subcellular Localization
Gajendra P.S. Raghava
Saturday, 06 December 2008 20:23 UTC
Hi, In past number of methods have been developed for predicting subcellular location of a protein. Recently, we also developed a subcellular method ESLpred2 . In general new methods are technically sound and more accurate than previous methods. Publishing a paper is one issue and its application in real-life is another issue. Publishing any technically sound paper is not very difficult in any bioinformatics journal. The question is whether it is worth to publish too many papers on subcellular localization.
I wants to know from group members particularly biologist whether they are using these methods for their research work or not. I always feel that bioinformatician should develop method useful for experimentalists not simply technically better methods. I will highly appreciate if you please send your comments whether these methods have any use for biologist or any experimental scientists.
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Replies
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Hi there,
I dont claim to be the most well informed on these matters… however, I take an interest in informatics and systems biology.I see it like this: for my purposes subcellular localization is important information when considering the validity of an interaction network.
I use cytoscape with some frequency, to troll interactome data and especially to view enrichment in GO tags amongst proposed networks / hubs / nodes.
Being able to superimpose subcellular localization data (or prediction) presents another criteria by which I can determine / evaluate the likely relevance / validity of a proposed interaction network that I have fished out of (often low quality) interactome data.
I would use any method that was available as a featured plug-in for cytoscape for sure.
Hope this feedback helps.
Cheers,
John -
Thanks for your input. Your input give me idea to use subcellular localization prediction in developing method for predicting protein-protein interaction.
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Hi,
We do use these methods. Mostly we work on protein-protein interactions in context of virus infection of host cell. We find some proteins change their localization (eg. cytoplasmic to Nuclear or vice versa)in some conditions. Could there be some common feature in these? Some yet to be identified signal. If these are analyzed, may be something can be found. I don’t know. May be, may be not. Just a thought.
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