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I am interested in collecting the reference genomes of marine protists and would like to know which databases can be used for such tasks, and is there a single, centralized database of protistological genomic data?

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    $\begingroup$ Hi and welcome to the site. Please not that asking for "the most commonly used" isn't a good question for this site since it will almost always require opinion-based answers ("I use database foo!"). A better question would be to tell us what you want to do and ask how to do it instead of asking for the most popular DB. That said, please edit your question and clarify what you want to do. Are you looking for the reference genome of specific species? What kind of analysis are you thinking of? What species? Protists? Fungi? Algae? What kind of info would a database have? $\endgroup$
    – terdon
    Jul 5 '17 at 9:12
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You can find many protist genomes on ensembl

http://protists.ensembl.org/index.html

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