distance calculation about big-scape HOT 6 CLOSED

Hi
We basically combine three indices to make up for the distance calculation. You can read more details about this in the Online Methods of the publication (free version: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6917865/#S9title) and in the Supplementary Note 1 section of the second supplementary file

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Thanks for your reply. I surely read the Supplementary Note 1 and the methods section of the article, and I know that three indices were used for distance calculation, but how the three indices were combined? It seems not shown in the paper. Does it like the following formula shows?
JwJaccard index + DSSwDSS index + AIw*Adjacency index

Another question is that how I should choose the threshold cutoff to build the BGCs network? The default cutoff is 0.3 in your paper, while 0.65 was used in another research project (Global analysis of biosynthetic gene clusters
reveals conserved and unique natural products in entomopathogenic nematode-symbiotic bacteria)

Thanks again!

from big-scape.

Indeed, the three indices were combined using different weights, which were calculated per biosynthetic class (see "Weight optimization methods" and the sections in the supplementary file mentioned therein)

The question of the cutoff is difficult. Our colleagues found 0.3 to be a good starting point due to its metabologenomic score while using known data, but each case might be different depending on the taxonomic diversity (or particular sub-biosynthetic class). My suggestion would be to add a couple of cutoffs above 0.3 and manually decide which works best for your data

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That's helpful. Thanks!

from big-scape.

That's helpful. Thanks!

from big-scape.

Great to hear!

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