I have screened a cDNA library of swine. I want to perform gene ontology on the obtained gene sequences so that a pie diagram representinbg the proportion of genes participating in various processes, functions and compartments can be made.
Alternatively, if you want to avoid these steps, you may use simply use blast2go which is java based and connects online through server. You may further use tools like EasyGO/DAVID!
Hi polite researcher (for "please"); try this, I do not know whether it is complete as a database, but I used it with good results for DNA/protein sequence.
http://goblet.molgen.mpg.de/cgi-bin/goblet2008/goblet.cgi?menu=Intro
If you have a gene list Aamir gave you a good advice.
i have the list of official gene symbols (45 in no.). i am not interested in performing enrichment analysis. i just want to functionall categorize them in GO Slim terms
AmiGo2 --> Term Enrichment Service (see link)
It isn't specific for swines, but includes several mammals.
Otherwise try any of these web GO tools:
http://neurolex.org/wiki/Category:Resource:Gene_Ontology_Tools
Good Work
http://amigo.geneontology.org/amigo
Hi,
It may be that not all of the protein coding sequences that you have predicted have an entry in UniProt. So in order to get a functional prediction for these sequences, you should search them using InterProScan. This is the tool used by UniProt to characterise new sequences that have no other published information associated. This will give you a list of possible functions (including GO terms) for the sequences.
I'm not sure what you mean by "to the 3rd level" as GO is a graph-based structure and the same terms may be at multiple levels in the graph. If you have a slim, you can apply it to the InterProScan results - contact the InterProScan team for help with this
Cheers
Sarah
http://www.ebi.ac.uk/interpro/interproscan.html
http://www.ebi.ac.uk/support/interpro-general-query
Thanks sarah. is there any tool where I can upload the whole gene list and get the GO annotation (BP, MF and CC) in a pie chart or bar diagram.
you could use http://david.abcc.ncifcrf.gov, this site allows you to select the level of GO annotation, cluster genes by GO terms. After annotation just take the terms and ho to excel to produce a pie chart or bar diagram.
The interpro team created a google charts-based tool for viewing metagenomics results for each subset of the GO (based on a slim) - see https://www.ebi.ac.uk/metagenomics/sample/SRS086444#ui-id-9 as an example (scroll down to the bottom of the page for the GO stuff). I'm sure they would be happy to share the code with you if you are interested.
https://www.ebi.ac.uk/metagenomics/sample/SRS086444#ui-id-9
Dear
I recommend Blast2GO - Software for Biologists
https://www.blast2go.com/b2ghome
Blast2GO® is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data.
Sonalika, I used BLAST2GO to annotate 30k sequences that I was working with. It is very suitable for your purposes, and allows you to do a lot of the things that everyone is suggesting, on one platform.
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