Question: Batch Download Enzymes by EC Number
0
gravatar for irazoqui.matias
2.4 years ago by
irazoqui.matias10 wrote:

Hi, I have many lists of EC numbers, that look like this:

ec:1.13.11.1; ec:1.14.12.10; ec:1.14.12.13; ec:1.14.13.50; ec:1.21.1.2; ec:1.3.1.25; ec:1.3.1.32; ec:3.1.1.45; ec:3.5.5.6; ec:3.8.1.7; ec:4.2.1.84; ec:5.5.1.1; ec:5.5.1.7; ec:6.2.1.33

And I'd like to download all the corresponding sequences from UniProt (it could be another database, but I like the annotation quality of SwissProt). I've looking for a way to batch download these, but I couldn't find any. It's really easy to do it via website, but it gets annoying when you have many EC numbers.

Is there any script or tool to do it automatically?

Thank you!

uniprot sequence ec number • 909 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by irazoqui.matias10
1
gravatar for irazoqui.matias
2.4 years ago by
irazoqui.matias10 wrote:

I found a way to do with BASH:

while read line; do
    wget "http://www.uniprot.org/uniprot/?sort=&desc=&compress=no&query="$line"&fil=&format=fasta&force=yes"
done < "list.txt"

But I don't know if there's another, more efficient way to do it

ADD COMMENTlink written 2.4 years ago by irazoqui.matias10

Yes, this RESTful programmatic access is an approach we would have recommended at the UniProt helpdesk. See also

in case you hadn't noticed these documents yet.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Elisabeth Gasteiger1.7k
0
gravatar for lessismore
2.4 years ago by
lessismore730
Mexico
lessismore730 wrote:

I think you may find useful infos here Convert kegg ids to uniprot ids

ADD COMMENTlink written 2.4 years ago by lessismore730
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