Question: From GI to GO anootations
0
gravatar for benarnon
3.3 years ago by
benarnon20
Israel
benarnon20 wrote:

Hi. I have a long list of GI which I want to retrieve their GO annotations. I read that one way to do it is by converting the GI identifier into UniPortKB identifier and from there to retrieve the GO annotations. I tried to do so by using the uniprot_tools 0.4.1 where I mapped the GI into UniProtKB and then retrieved the UniProt object.

For some of the GI's it worked but for some get the following message : Sorry, no results were found. You mapped from GI number to UniProtKB. However, 1 was successfully mapped to the UniParc sequence archive. View UniParc results (1)

When I looked on the UniParc result I get the following table: http://www.uniprot.org/uniparc/?query=yourlist:M20161020F725F458AC8690F874DD868E4ED79B8896594EO&sort=yourlist:M20161020F725F458AC8690F874DD868E4ED79B8896594EO&columns=yourlist(M20161020F725F458AC8690F874DD868E4ED79B8896594EO),id,organisms,kb,first-seen,last-seen,length

First, anybody can explain me what exactly is the different between UniPARC and UniPortKB. Second, what am I suppose to do with the table and how can I get the GO annotations?

uniprot gene • 1.0k views
ADD COMMENTlink modified 3.3 years ago by Elisabeth Gasteiger1.7k • written 3.3 years ago by benarnon20

UniParc and UniProt from Wikipedia

ADD REPLYlink written 3.3 years ago by Sej Modha4.6k
0
gravatar for Mahmut Uludag
3.3 years ago by
KAUST, Thuwal, Saudi Arabia
Mahmut Uludag10 wrote:
ADD COMMENTlink written 3.3 years ago by Mahmut Uludag10
0
gravatar for Prasad
3.3 years ago by
Prasad1.6k
India
Prasad1.6k wrote:

try db2db from biodbnet.

ADD COMMENTlink written 3.3 years ago by Prasad1.6k
0
gravatar for Elisabeth Gasteiger
3.3 years ago by
Geneva
Elisabeth Gasteiger1.7k wrote:

Here is some general documentation about UniProtKB and UniParc http://www.uniprot.org/help/uniprotkb http://www.uniprot.org/help/uniparc

However, since your query seems to involve bacterial entries (cf the UniParc entry in your query http://www.uniprot.org/uniparc/UPI00001B8619):

There are 65 Bordetella bronchiseptica proteomes, but only 4 of them are non-redundant: http://www.uniprot.org/proteomes/?query=organism%3A%22bordetella+bronchiseptica%22&sort=score The redundant ones (cf http://www.uniprot.org/help/proteome_redundancy_faq) can only be found in UniParc.

See also: http://www.uniprot.org/help/redundancy

ADD COMMENTlink written 3.3 years ago by Elisabeth Gasteiger1.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 620 users visited in the last hour