E.C. numbers to GO terms or annotations

Question

[shibl_a]

I have a list of E.C. numbers (~200) that I would like to 'translate' into either GO terms or, even better, annotation descriptions. Is there a platform/ software on which I can submit that list as input and get their description as output? Thanks!

[cpad0112]

Please post some example EC numebers.

[shibl_a]

here is part of the list:

EC:1.1.1.100 EC:1.1.1.27 EC:1.1.1.29 EC:1.1.1.35 EC:1.1.1.38 EC:1.1.1.39 EC:1.1.1.79 EC:1.1.1.8 EC:1.1.1.81 EC:1.1.1.86 EC:1.1.1.94 EC:1.1.1.95 EC:1.10.2.2

Answer 1

[lieven.sterck]

There is a 'conversion' list provided by the EBI, you can find it by linking though from here

[cpad0112]

i think mapping is redirected to this page from EBI: http://www.geneontology.org/external2go/ec2go

[lieven.sterck]

indeed it is, but I pointed to the 'intro' page (which also gives a bit of background info). Will edit my answer

[cpad0112]

you are correct that you provided correct link (with background and every thing). Link I posted was for impatient users :). @Lieven

[shibl_a]

Thanks! I came across this earlier but I would have to manually search for each EC number on it's own. That would work if I had a few to deal with, but given that my list is quite long I was looking for more of a program that would give me the output we see on the page from EBI.

[Fatima]

This command converts GO2EC, but you can easily modify it to convert EC2GO.

Provide the path to ec2go mapping file:

ec2go = home + "/data/ec2go"

awk 'FNR==NR{go2ec[$NF]=$1; next} { if ($2 in go2ec) { ec=go2ec[$2]; n=split(ec, t, "."); ecshow=substr(ec, 4); for(i=n+1;i<=4;i++) ecshow=ecshow".-"; print $1 " " ecshow; }}'  ec2go  gofile   >  ecfile

https://sourceforge.net/p/fun4me/code/ci/master/tree/fun4me.py

Also, you can use Minpath tool to convert EC numbers to metabolic pathways. It's included in the above package.

[lieven.sterck]

Simply use grep or awk or such to select the lines (ECnumbers) you need based on your input list