What Is The Easiest Way To Download All Results From An Ncbi Est Query?

Question

[John]

I've queried the EST database at the NCBI and I get back ~1000 results. see here: http://www.ncbi.nlm.nih.gov/nucest?term=txid2%5Borgn%5D%20AND%20gbdiv_est%5Bprop%5D

I'd like to download all sequences as a FASTA file, but I can't find a link to do this on the website.

I've tried using a Fetch perl script, with this query

$query = 'txid2[orgn]+AND+gbdiv_est[prop]';

but, I do not get any results: http://www.ncbi.nlm.nih.gov/books/NBK25498/#chapter3.ESearch__ESummaryEFetch

What's the easiest way to do this?

Cheers, John

Answer 1

[Neilfws]

There is a link on the website to do this.

On your results page, at the top on the right hand side, look for a link that says "Send to". Click on the down-arrow to expand the link and select "File". The box will expand; use the selection list under "Format", choose "FASTA" and click "Create File".

[John]

Thanks Neil, I'm an idiot, I think that in the past that link only downloaded the sequences on the current page, anyhow, that's great! Thanks.

[Neilfws]

You're welcome. I think there was a time when the download link did not retrieve all results (and Batch Entrez was recommended) but now, all search results are retrieved. It can take a while, depending on number of results.

[Michael Schubert]

And there I was thinking you had to put a checkmark on all results before... glad to see it work this way :-)

Answer 2

[Michael Schubert]

You need to do an ESearch first which yields you a list of IDs

http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucest&term=txid2[orgn]+AND+gbdiv_est[prop]

This you can then use to EFetch/ESummary your results

http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucest&rettype=fasta&id=1053200,325152494,325152492

This is using the NCBI EUtils directly. In Perl, you can either query the URLs the same way or use the functions provided in BioPerl (see the docs).

And as you asked for the easiest version, I'm not going to tell you about history-enabled search ;-) but that would be in the NCBI docs as well