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download protein sequences from NCBI

Hi all,

I would like to download all protein sequences from one species on NCBI:

https://www.ncbi.nlm.nih.gov/protein?linkname=bioproject_protein&from_uid=261773

This is maybe trivial, but is there a way to download all sequences concatenated in only one fasta?

Thanks a lot,

Guillaume

fasta ncbi protein
• 7,489 views • link
updated by Kevin Blighe Kevin Blighe • written by guillaume.rbt guillaume.rbt

there is a send to option through which you can download all the sequences. After just remove the fasta headers to make a single fasta

awk 'BEGIN{a=0}{if($0~/^>/){if(a==0){print}a++;}else{print}}' input.fasta >out.fasta
• 1 views • link
written by Prasad Prasad

thanks for the response, how do you use the send to option? Is this on the console or on the website?

• 1 views • link
written by guillaume.rbt guillaume.rbt

4 answers

using the ncbi interface you can just click on "Send to > File"

or using eutils:

curl "http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=bioproject&id=261773&linkname=bioproject_protein"  | xmllint --xpath '//LinkSetDb' - | xmllint --format - | grep "<Id>" | cut -d '>' -f 2 | cut -d '<' -f 1 | while read L; do curl "http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=${L}&rettype=fasta" ; done

>gi|821074095|gb|KKY28990.1| putative uracil phosphoribosyltransferase [Diplodia seriata]
MFVHASGPESIKFKHLQGQVQVLLVDSVINSGATILDFVEAIREINPGIRIVVVAGTVQAQCISPNNPFY
KTLAQHGDISLVALRSSETKFTGSGGTDTGNRLFNTTHLL

>gi|821074094|gb|KKY28989.1| putative integral membrane protein [Diplodia seriata]
MPQYFPWPYSVDPLPEDLRRGLWPVGIFALMSTVATLALLCWITYRLVSWRKHYRSYVGYNQYVLLIYNL
LLADLQQSISFLISFHWIHTDSMLAPSPACFGQAWLVQIGDISSGMFVLAIALHTFFSVVKGRQIPFRAF
LIGTIVIWALALLLTVLGPALHGSDYFTAAGAWCWASDKYETERLWLHYLWIFIIEFGTVIIYALIFIYL
RKQLVSIASAHQHSTQNKVSQAARYMVLYPLTYVLLTLPLAAGRMATMTGQTLPIAYYCAAGSMMTSCGW
VDAALYALTRRVLVSNEIDQPQGGAGKGASSSGGRTGYGGHGSSHTATGWDIASFSDRKGGMGADHSVTI
TGGLDARGSNFIDMDELSKGGVHHHATERVGRPKHKGSSTPSTQGLTRARSSSTSARESTPRGSTDSILA
GLGGVRAETKVEIRVEPANGFMLPGEGSGSNGSSGMSTPNGRTVEVVGNSHAMRPRSGSPY
• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Here is a well-explained tutorial for your problem :)

• 1 views • link
written by tlorin tlorin

The link you provided doesn't seem to work.

• 1 views • link
written by Sej Modha Sej Modha

This should be better now, thanks!

• 1 views • link
written by tlorin tlorin

thank you all for your help! works fine

• 1 views • link
written by guillaume.rbt guillaume.rbt

NCBI Unix e-utils version of the @pierre's solution

esearch -db bioproject -query 261773|elink -target protein |efetch -format fasta
• 1 views • link
written by Sej Modha Sej Modha

Another solution(s) implemented as a Python script:

Kevin

• 0 views • link
written by Kevin Blighe Kevin Blighe

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