Refseq proteins for several taxids
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6.2 years ago
seta ★ 1.5k

Hi all,

My question may sound simple. I'm trying to download the plant ref-seq proteins from NCBI to make blast database and run blastx for contigs resulted from de novo assembly of a non-model plant. As there is several taxonomy ID for plants, like flowering plants (3398), green plants (33090), ...please be ware me how I can get all plant ref-seq protein sequence to have as rich as database? please don't refer me to ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plant/ as it contains mixed refseq sequences, not just protein refseq. thanks in advance. 

 

blast RNA-Seq next-gen • 2.6k views
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6.2 years ago
Siva ★ 1.8k

You can download only the protein sequences from the FTP URL you listed using curl.

curl -o plant.#1.protein.faa.gz ftp://ftp.ncbi.nlm.nih.gov/refseq/release/plant/plant.\[1-87\].protein.faa.gz

 

 

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Thanks a lot friend. Is there similar command to get the plant protein sequences from Uniprot?

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The following query will retrieve all sequences with keyword "Complete Proteome" from the taxonomy group "Viridiplantae".

http://www.uniprot.org/uniprot/?query=taxonomy%3A%22Viridiplantae+[33090]%22+keyword%3A%22Complete+proteome+[KW-0181]%22
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