Creation of Fasta Database of Bacterial Proteins

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7.7 years ago

rlee03 • 0

Hi,

I tried creating a Fasta Database using an Entrez Query but I consistent get booted from the NCBI server due to the large request. Can you recommend another way to download all the proteins bacteria in a fasta file that should work? n=5.8 million

Thanks!

I'm a python programmer and prefer to do this via the command line

blast blastp proteins fasta • 2.1k views

ADD COMMENT • link updated 4.1 years ago by Biostar 20 • written 7.7 years ago by rlee03 • 0

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You can download many (all?) bacterial genomes here: ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria Getting protein sequences from bacterial genomes is most probably trivial for you ...

ADD REPLY • link 7.7 years ago by Protostome ▴ 50

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You could get all RefSeq proteins by downloading the faa protein files here.

Get the protein files from folder hierarchy from link posted by @Protostome: ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/name_0f_bacteria/latest_assembly_versions/GCA_*/*faa.gz files.

ADD REPLY • link 7.7 years ago by GenoMax 147k

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How to download all the parasite protein data from NCBI?

ADD REPLY • link 7.7 years ago by shenwei356 8.7k

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