Blast2Go Pro questions

[Jacob_Neckel]

Hello,

I am new to using blast and have successfully uploaded a FASTA file. My questions (a little silly) regards with interpreting the data, specifically the graphs (pie, bar).

When I create a graph it asks me to select a level. I have done some searching and have not found what it means by "level of graph nodes." Is this meant in the mathematical vertices sense? Some levels have a huge abundance of protein functions than others and some levels include different types of proteins (binding proteins for the lower levels and membrane transport proteins in the higher levels). Can someone explain levels to me in a simplified way or send me a link that will help me?

Second, what does it mean on the top y-axis by "#Seqs"?

Thanks for answering my silly questions!

[SES]

These are good things to ask the company since you paid for the product. It's not a bad idea to ask here but I think you'll get a faster and likely more accurate answer by just asking the blast2go people.

[sgoetz]

Hi Jacob.
Yes, "level" means in this context the distance (vertices) from a GO term to the root term.
Indeed, the use of levels to summarize information in the Gene Ontology, which is a direct acyclic graph, is not always suitable, in part for the reason you already mentioned: The level of a GO term does not define its specificity.
In Blast2GO there are two alternative options:
One is the use of GO-Slim, a way to reduce the functional information of a annotation dataset to a fixed, smaller and more general subset of GOs. http://geneontology.org/page/go-slim-and-subset-guide
Another option is the MultiLevel charts, which allows to "cut through" a GO graph depending on the amount of sequences assigned to a GO node/term or the relevance of the terms independently to its level.

Regarding your second question: The hash character is used as a short form for "number of". In this case "number of sequences".

Best. S.

[sgoetz]

Hi SES.
Blast2GO is freely available for academics in the basic version. You can register and download it from here: https://www.blast2go.com/blast2go-pr...register-basic
Its allows NCBI Blast, InterPro, GO mapping, functional annotation, GO graph visualisation, Enrichment Analysis etc.
The PRO version which offers additional features and resources requires a paid subscription.
Best, S.