Question: Protist in UniProt/NCBI taxonomic tree
0
gravatar for Seq225
3 months ago by
Seq22590
Seq22590 wrote:

I am trying to do horizontal gene transfer analysis. I want to download the Protist (Protista) sequences from UniProt.

Protists are eukaryotes, and they are a kingdom. Protist is one of the six kingdoms of life. However, I am having some difficulties downloading their sequences from UniProt. I see different Protist taxid in NCBI, such as:

uncultured eukaryotic protist (taxid:1295078) uncultured protist (taxid:1295078) unidentified protist 56059 (taxid:56059) ... ......

Would someone help me to determine how to download the entire set of Protist sequences (the entire Protist kingdom) from UniProt?

Thanks a lot!!

assembly alignment genome gene • 161 views
ADD COMMENTlink written 3 months ago by Seq22590
1

Try - http://protists.ensembl.org/info/website/ftp/index.html

ADD REPLYlink written 3 months ago by aditi.qamra260

Thanks. The link is very useful. Probably, what I need is here.

ADD REPLYlink written 3 months ago by Seq22590
1

Try this link: http://www.phytopathdb.org/pathogens_eg

They have some Protist genomes:

http://www.phytopathdb.org/content/albugo-candida

http://www.phytopathdb.org/content/albugo-laibachii

http://www.phytopathdb.org/content/hyaloperonospora-arabidopsidis

http://www.phytopathdb.org/content/phytomonas-sp

http://www.phytopathdb.org/content/phytophthora-infestans

http://www.phytopathdb.org/content/phytophthora-kernoviae

http://www.phytopathdb.org/content/phytophthora-lateralis

http://www.phytopathdb.org/content/phytophthora-parasitica

http://www.phytopathdb.org/content/phytophthora-ramorum

http://www.phytopathdb.org/content/phytophthora-sojae

http://www.phytopathdb.org/content/pythium-aphanidermatum

http://www.phytopathdb.org/content/pythium-arrhenomanes

http://www.phytopathdb.org/content/pythium-irregulare

http://www.phytopathdb.org/content/pythium-iwayamai

http://www.phytopathdb.org/content/pythium-ultimum

http://www.phytopathdb.org/content/pythium-vexans

Browse those genomes in the Ensemblr Genomes website(brown link at the bottom of each page after Description)

These ones above are only pathogenic.

ADD REPLYlink modified 3 months ago • written 3 months ago by natasha.sernova3.4k
1

I don't think these are protists at all. They are oomycetes.

Phytophthora is morphologically very similar to true fungi yet its evolutionary history is completely distinct. In contrast to fungi, SAR supergroup is more closely related to plants than to animals. Whereas fungal cell walls are made primarily of chitin, Phytophthora cell walls are constructed mostly of cellulose.

Ensembl appears to consider them protists since they have included the sequences in Protist genomes page.

Seq225 : You will need to decide if you like that classification.

ADD REPLYlink modified 3 months ago • written 3 months ago by genomax65k

Thanks. I guess the link provided by aditi.qamra has the sequences. However, I am having some trouble downloading files from that server. Hopefully will get it eventually.

ADD REPLYlink written 3 months ago by Seq22590
1

Seq225 : Are you using the link I posted above for the genomes page?

ADD REPLYlink written 3 months ago by genomax65k

Yes, its actually the same one that aditi posted.

However, what I see in UniProt is that all the taxonomic branches do not contain sequences in a exclusive fashion (probably same applies to Ensembl). I need all metazoan in one file and everything else in a different files. Therefore, some filtering on the downloaded files will probably do the trick.

Thanks for providing the very useful links!!

ADD REPLYlink written 3 months ago by Seq22590

Thank you very much Natasha.

ADD REPLYlink written 3 months ago by Seq22590
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