I've annotated 580 sequences and now like to select a subset (to then export it, retrieve the sequence ID's and run Fisher's exact). However I am stuck already with the first step. Clicking on Select I have tried Select by Sequence Name/ID, Select by Sequence Description and Select by Functions (GO-Terms or GO-IDs) - the last one, is what I want - but writing e.g. "protein binding" in the text field I am always either getting zero selections. What I really wanted is select all sequence that have "developmental process" annotated (which is a level 2 biological process). Putting this in the text box usually selects all 580 sequences. To tackle the problem differently: is there a way to export data not with the parental GOs but derived ones (like "developmental process") I could then just get my sequence IDs from the the textfile?
On Wednesday, August 22, 2012 11:23:45 AM UTC+2, Phil wrote:
> Hi!
> I've annotated 580 sequences and now like to select a subset (to then > export it, retrieve the sequence ID's and run Fisher's exact). However I am > stuck already with the first step. Clicking on Select I have tried Select > by Sequence Name/ID, Select by Sequence Description and Select by Functions > (GO-Terms or GO-IDs) - the last one, is what I want - but writing > e.g. "protein binding" in the text field I am always either getting zero > selections. What I really wanted is select all sequence that > have "developmental process" annotated (which is a level 2 biological > process). Putting this in the text box usually selects all 580 sequences. > To tackle the problem differently: is there a way to export data not with > the parental GOs but derived ones (like "developmental process") I could > then just get my sequence IDs from the the textfile?
Dear Phil,
the select option in Blast2GO is "accumulative" or "additive". So one
selection can be added to another. If you want to select something you have
first to deselect all. If you want to select everything below a term
(derived ones):
- deselect everything
- use select by go-id
- type GO:0032502 for developmental process
- select "include go parents". This means if a term has developmental
process as parent it will be selected - > all seqs which are annotated
with developmental process or more specific terms will be selected.
Regards,
Stefan
On 23 August 2012 15:20, Phil <philipp.schif...@gmail.com> wrote:
> Hi there!
> This seems to be a Mac Problem. I can select said sequences from the same
> dataset on my SL Linux (run through XQuartz).
> Phil
> On Wednesday, August 22, 2012 11:23:45 AM UTC+2, Phil wrote:
>> Hi!
>> I've annotated 580 sequences and now like to select a subset (to then
>> export it, retrieve the sequence ID's and run Fisher's exact). However I am
>> stuck already with the first step. Clicking on Select I have tried Select
>> by Sequence Name/ID, Select by Sequence Description and Select by Functions
>> (GO-Terms or GO-IDs) - the last one, is what I want - but writing
>> e.g. "protein binding" in the text field I am always either getting zero
>> selections. What I really wanted is select all sequence that
>> have "developmental process" annotated (which is a level 2 biological
>> process). Putting this in the text box usually selects all 580 sequences.
>> To tackle the problem differently: is there a way to export data not with
>> the parental GOs but derived ones (like "developmental process") I could
>> then just get my sequence IDs from the the textfile?
>> Cheers
>> Phil
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Recently the NCBI server is very slow for blasting. The worst case is that processing 24 hours just got 3 seqs done! Do you have similar experience?
Thanks.
Jun-Jun Liu
********************************************
Dr. Jun-Jun Liu
Research Scientist / Chercheur scientifique
Government of Canada / Gouvernement du Canada
Natural Resources Canada / Ressources naturelles Canada
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