GO term

[vcastroagudin]

Hello,

I have noticed that The GO terms that come out from FUNANNOTATE do not match with the term that results from Running emapper v2 by itself in its own website. Does someone know why? Which is the correct GO term to use?

for example, from funannotate I get

CT692_000051 -> GO:0016021

And from EggNog website:

CT692_000051-> GO:0000322,GO:0000323,GO:0000324,GO:0003674,GO:0003824,GO:0004012,GO:0005215,GO:0005319,GO:0005548,GO:0005575,GO:0005622,GO:0005623,GO:0005737,GO:0005773,GO:0005783,GO:0005886,GO:0006810,GO:0006811,GO:0006812,GO:0006820,GO:0006869,GO:0008150,GO:0009987,GO:0010876,GO:0012505,GO:0015695,GO:0015696,GO:0015711,GO:0015748,GO:0015914,GO:0016020,GO:0016021,GO:0016043,GO:0016462,GO:0016787,GO:0016817,GO:0016818,GO:0016887,GO:0017111,GO:0031224,GO:0033036,GO:0034204,GO:0042623,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0043492,GO:0044424,GO:0044425,GO:0044444,GO:0044464,GO:0045332,GO:0051179,GO:0051234,GO:0061024,GO:0065007,GO:0065008,GO:0071702,GO:0071705,GO:0071840,GO:0071944,GO:0097035,GO:1905329

->

--

Thanks,

Vanina

[Cantalapiedra]

Hi,

I am not sure whether the eggnog-mapper version and command is the same in funannotate than in the online version of eggnog-mapper. Also, the GO term you obtain with funannotate is from eggnog-mapper or from interproscan results? In the online version of eggnog-mapper, is important for interpretation the taxonomic scope parameter. Notice that those GO terms are transferred from all the orthologs found within that taxonomic scope. This can be further constrained using eggnog-mapper command line tool using the target_taxa parameter. In conclusion, those GO terms would be the functions in which the all the genes in the orthologous group matched by your query are involved.

Best, Carlos

[vcastroagudin]

Thank you Carlos. This helps a lot.

Vanina

On Thu, Aug 27, 2020 at 3:36 AM Carlos P Cantalapiedra < notifications@github.com> wrote:

Hi,

I am not sure whether the eggnog-mapper version and command is the same in funannotate than in the online version of eggnog-mapper. Also, the GO term you obtain with funannotate is from eggnog-mapper or from interproscan results? In the online version of eggnog-mapper, is important for interpretation the taxonomic scope parameter. Notice that those GO terms are transferred from all the orthologs found within that taxonomic scope. This can be further constrained using eggnog-mapper command line tool using the target_taxa parameter. In conclusion, those GO terms would be the functions in which the all the genes in the orthologous group matched by your query are involved.

Best, Carlos

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-- Vanina L. Castroagudín, PhD

Postdoctoral Researcher

Mycology & Nematology Genetic Diversity & Biology Laboratory

USDA - ARS

10300 Baltimore Avenue, Bldg 10A, Room 227

Beltsville, MD 20705

Cell: (479) 313-3780

Vanina.Castroagudin@usda.gov vanina.castroagudin@usda.gov

v.castroagudin@gmail.com v.castroagudin@gmail.com

[Cantalapiedra]

You are welcome.

I will close the issue, please re-open in case you wish to ask more about it.