Fungi genomes: which database should I use?
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3.5 years ago
tlorin ▴ 330

Hello,

I don't work on fungi - at all. However, it happens that I have to dive into this lineage to understand the evolution of a gene that I thought would be specific to animals, but is not.

I have found many resources that seem to harbor genomic resources on fungi. I can think of the JGI portal, the FungiDB platform, the dedicated Ensembl Fungi or even the NCBI FTP with fungal genome sequences. Each of them seems quite documented about fungi genomes but they seem different. For instance, the genome of Hypsizigus marmoreus is not on JGI but is available on Ensembl Fungi.

Does anyone working on fungi know the differences between these platforms? Which one should I use if I want to blast an animal protein on the fungi lineage?

Many thanks for your help!

fungi genome blast ensembl jgi • 1.4k views
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You could extract all sequences assigned a fungal TaxID (4751) and blast against those sequences.

Edit: While they don't make it easy you should be able to download data after creating an account.

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Indeed it's not very easy to access this data.

You could extract all sequences assigned a fungal TaxID (4751) and blast against those sequences.

Could you elaborate on this? Do you mean in NCBI? Thanks!

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See Neilfws answer here.

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(By the way, I have found the web interface of JGI to be VERY slow when blasting on the whole fungi lineage.)

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