Request to add Hessian fly to Cluego

[kve...@gmail.com]

I would like to add the Hessian fly (Mayetiola destructor) to Cluego.

I read in the FAQ section that the files are based on information from KEGG, GO, Uniprot-GOA annotations, and NCBI; however, I don’t think the Hessian fly (my organism) gene set has been submitted to these databases. The Official Gene Set files (GFF and fasta files with the nucleic acid and translated amino acid gene sequences) are available on the i5k workspace: 

https://i5k.nal.usda.gov/sites/default/files/data/Arthropoda/maydes-%28Mayetiola_destructor%29/Current%20Genome%20Assembly/2.Official%20or%20Primary%20Gene%20Set/OGS1.0/hf_ogs.gff

https://i5k.nal.usda.gov/sites/default/files/data/Arthropoda/maydes-%28Mayetiola_destructor%29/Current%20Genome%20Assembly/2.Official%20or%20Primary%20Gene%20Set/OGS1.0/hf_OGS1.0.cds.fasta

https://i5k.nal.usda.gov/sites/default/files/data/Arthropoda/maydes-%28Mayetiola_destructor%29/Current%20Genome%20Assembly/2.Official%20or%20Primary%20Gene%20Set/OGS1.0/hf_OGS1.0.pep.fasta

Is it possible for me to add the Hessian fly gene set anyway? 

[Scooter Morris]

Hi Karen,

   I've passed your request off to the ClueGO authors.

-- scooter

[Bernhard]

Hi,

In ClueGO we use publicly available data from UniProtKB, and NCBI. To create a new organism we need to know its taxonomy id (https://www.ncbi.nlm.nih.gov/taxonomy), and to have ontology information. In the links you posted I could not see this.

Some ClueGO users obtained custom functional annotations using software like: the EggNOG mapper:

https://academic.oup.com/mbe/article/34/8/2115/3782716

http://eggnogdb.embl.de/#/app/emapper

To create ClueGO custom annotation files we need gene/protein ids and their corresponding GO ids GAF formatted, or as a tab delimited file.

Best,