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Old 12-12-2015, 09:58 PM   #1
maryam
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Default Get complete protein sequence

Hi all,

Could you please let me know how I can download the complete protein sequence of some plant species from ncbi, or anywhere that you suggest? Sorry for this basic question.
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Old 12-13-2015, 03:50 AM   #2
mastal
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See the NCBI RefSeq ftp site,

http://www.ncbi.nlm.nih.gov/refseq/

you can download the plant protein .faa format files.

but that will give you all the proteins for all plants.

If you select the Proteins reaource from NCBI, and put in the plant you are interested in, for example, 'Arabidopsis thaliana',
you will get all the arabidopsis protein files, and there is an option at the top of the page to save the results to a file, with
options for format, so if you want the sequences, select, fasta.

http://www.ncbi.nlm.nih.gov/protein?...%5BOrganism%5D

Last edited by mastal; 12-13-2015 at 04:05 AM.
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Old 12-13-2015, 10:36 AM   #3
maryam
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Thanks for your reply. I knew this way to get the protein sequence, my problem is getting just complete (full-length) protein sequences of the organism of interest, say citrus sinensis. Please let me know the right way to this end, I'm familiar with linux command, so please feel free to put the right command if there is. Thanks in advance
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Old 12-13-2015, 02:13 PM   #4
GenoMax
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If you need the proteins of Citrus cinensis in fasta format you can find the file here: ftp://ftp.ncbi.nlm.nih.gov/genomes/a...protein.faa.gz

You can use wget/curl to download this file via the command line and the link above.

Genome for Cirtus cinensis is here: http://www.ncbi.nlm.nih.gov/genome/?...itrus+sinensis
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Old 12-13-2015, 03:06 PM   #5
maryam
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Thanks for the reply. As I mentioned in the post and my previous reply, I'm looking for only complete (full length) protein sequence, not any partial sequence. Please advise me on this way
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Old 12-13-2015, 11:28 PM   #6
SylvainL
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Then simply parse the file to remove the partial sequences (annotated as partial...)
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