third-party tools

Questions related to third-party tools (not AmiGO, OBO-Edit, etc.).

How can I programmatically get a list of GO terms associated with a gene identifier?

This very useful BIOSTARS thread clarifies "How Do I Do Simple GO Term Lookup Given A Gene (Or mRNA) Identifier?" You might find these responses useful when trying to simply create a list of GO terms associated with a given ID- and when you are not looking to conduct enrichment analyses - using a programatic approach. https://www.biostars.org/p/1226/

How can I do term enrichment analysis for a species that is not present in the list from AmiGO?

The Term Enrichment tool on the GO and AmiGO websites center only on data from the genomes available on the PANTHER Classification System Database (http://go.pantherdb.org). Details about how to use the tools available on AmiGO and how to interpret the results is available on our website at http://geneontology.org/page/go-enrichment-analysis.

How do I find all annotations for species X that I can't find in AmiGO?

  1. Open the QuickGO web-page http://www.ebi.ac.uk/QuickGO/
  2. Click on the Search and Filter GO annotation sets link located beneath the search box
  3. This will lead you to an Annotation download page where you can click the filter icon (Located to the right hand side of the page)

How do I annotate a de novo assembled transcriptome against the GO database?

You can annotate the coding sequences in your transcripts using InterProScan. You can do this using WebServices or by downloading the tool and running it locally. Details can be found at: http://www.ebi.ac.uk/interpro/search/sequence-search/

This will predict GO terms based on domains detected using the mapping file here: http://geneontology.org/page/download-mappings