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I have a list of A. thaliana proteins and I'd like to know their location in the cell. I've found SUBA but they seem not to share their dataset and only allow queries through their website. It's inconvenient for me, because I need to locate 1.6k of proteins and process the results further. Is there a dataset or an API I could use instead?

PS. If this is not the right forum to ask this, please notify me.

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If you click through to the actual SUBA4 publication, you can see in the data availability section that they have reposited source datasets from which their predictions are derived, at http://dx.doi.org/10.4225/23/581055ddcb1ce.

These appear to be standard e.g. CSV files of various data layers, such as here. It may take some effort (e.g. their algorithm) to integrate these data sources, I am not familiar with these datasets.

It is of course inconvenient that they don't choose to advertise this on the server itself.

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  • $\begingroup$ Thanks, I found it too, after posting here. I was hoping there was a link on their website I missed. $\endgroup$
    – micoay
    Nov 27, 2021 at 10:33
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You can also try using The Arabidopsis Information Resource (TAIR).

It is the database specifically created for model higher plant Arabidopsis thaliana.

You can download the files in .fasta, .gz, .txt, .csv formats from their DOWNLOAD WEBPAGE. The website also provides links to other A. thaliana information resources.

PS: The database is weekly updated.

Edit 1: Try this or track to download_files/Proteins/Properties/AtSubP_results

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  • $\begingroup$ That's where I looked first but I haven't found any file with protein locations. In an NCBI article about SUBA I've found a link to some .csv files used by the website, although they have to be cleaned to be usable. $\endgroup$
    – micoay
    Nov 27, 2021 at 10:28
  • $\begingroup$ can you point to where on TAIR specifically these localisome data reside? $\endgroup$ Nov 27, 2021 at 22:36
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    $\begingroup$ @micoay, I have added a link to my answer. Please let me know if it works for you. I'm assuming you already have the protein-ID list. $\endgroup$ Nov 28, 2021 at 5:07
  • $\begingroup$ Thanks, I missed this file. For people searching for the file on the website: Downloads/Proteins/Properties/AtSubP_results. $\endgroup$
    – micoay
    Nov 28, 2021 at 19:18
  • $\begingroup$ @micoay, If that has solved your problem, then please accept my answer by clicking a tick button on the left side of my answer on your forum. I would appreciate that. $\endgroup$ Nov 29, 2021 at 3:41

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