Question

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.

Answer 1

Consider using the PhosPhAt database, NCBI, or UniProt for batch queries on Arabidopsis thaliana protein localization. These databases might offer APIs or bulk download options suitable for processing large numbers of proteins.

Step-by-step explanation:

If you are looking for subcellular localization data on a large scale, such as for 1.6k Arabidopsis thaliana proteins, and SUBA is not practical for your needs, you might want to look into other resources or databases that offer bulk download options or APIs. One potential resource is the Arabidopsis phosphorylation site database PhosPhAt, which provides phosphorylation data that might include localization information. Additionally, databases like NCBI or UniProt might have the facilities for batch queries which could provide the subcellular location as annotated in protein metadata. While databases such as WallProtDB can provide insights into cell wall proteins, they might not cover the full spectrum of subcellular localizations. For high-throughput analysis, consider using bioinformatics tools designed for batch processing, or scripts that automate the submission and retrieval of data from these databases.Unfortunately, there is no specific dataset or API available for obtaining the subcellular location of Arabidopsis thaliana proteins.

The SUBA database, which is widely used for this purpose, does not share its dataset or provide an API.However, there are other resources and databases that you can use to predict the subcellular location of proteins. One such resource is the WallProtDB database, which provides information on cell wall proteins of various species, including Arabidopsis thaliana.In addition to database resources, there are also prediction tools available that can predict the subcellular location of proteins based on their sequence or physicochemical properties. Examples of such tools include TargetP, WoLF PSORT, and ChloroP. These prediction tools can help you predict the subcellular location of your list of Arabidopsis thaliana proteins.It is important to note that while these resources and tools can provide predictions, experimental validation is often necessary to confirm the subcellular localization of proteins.