How do you download a FASTA sequence from NCBI Nucleotide onto a remote server?

[ehlin]

I know this is probably really simple... but I want to download the fasta file for this gene onto my computing cluster:

http://www.ncbi.nlm.nih.gov/nuccore/NT_007914.14

I cannot find a download link to use 'wget' with, can anyone point me in the right direction?

Thanks,
Edwin

[nickloman]

If you do:

Display settings: FASTA

Send to: File

You get a link like this:

http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=on&log$=seqview&db=nuccore&dopt=fasta&val=51466650&extrafeat=0&maxplex=1

[maubp]

There is also the Entrez Utilities Fetch command, EFetch, which is probably using the same thing once it gets to the NCBI;

http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/efetch_help.html

Libraries like BioPerl and Biopython have an API to try and make this more friendly.

Also have a look at TogoWS - especially if based in Asia, as their URL API is really simple to use:

http://togows.dbcls.jp/site/en/rest.html

[ehlin]

Thanks for your replies, I will give them a try.

[tomybou]

I don't know if that was your problem but I also wanted to choose where to download this file : you have to look for the Preferences of your navigator and check something like : "always ask me in which folder to download files"

[cirosantilli]

wget 'https://www.ncbi.nlm.nih.gov/search/api/sequence/${accession}/?report=fasta'

works nowadays, e.g.:

wget -O NC_001416.1.fasta 'https://www.ncbi.nlm.nih.gov/search/api/sequence/NC_001416.1/?report=fasta'

downloads the lambda phage: https://www.ncbi.nlm.nih.gov/nuccore/9626243