Question: How to download all complete protein sequences from BLAST search
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gravatar for milnerk3
6 months ago by
milnerk30
milnerk30 wrote:

Hello, I am using tBLASTn to collect sequences. What I would like to do is download a txt file containing the complete protein fasta sequences for the results of each search, and also possibly a txt file with the nucleotide CDS in fasta.

My options on the page are download a sequence dump containing the complete genome of each organism, or a file containing only the aligned portions of each protein (ie - missing the ends in most cases). Is there a way to get the full protein sequences without individually looking up each result?

blast • 272 views
ADD COMMENTlink written 6 months ago by milnerk30

See the answers here: how to download all the complete genomes for mycobacteria from NCBI? (you will need to modify as needed) or how to download all protein sequnces of a bacteria using ncbi ftp site?

You will need to get the faa files to get protein sequence.

ADD REPLYlink modified 6 months ago • written 6 months ago by genomax69k
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