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Old 03-12-2012, 10:09 AM   #1
ehlin
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Default How do you download a FASTA sequence from NCBI Nucleotide onto a remote server?

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
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Old 03-12-2012, 11:07 AM   #2
nickloman
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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
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Old 03-12-2012, 12:14 PM   #3
maubp
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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/coreh...etch_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
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Old 03-12-2012, 06:37 PM   #4
ehlin
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Thanks for your replies, I will give them a try.
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Old 03-14-2012, 08:33 AM   #5
tomybou
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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"
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