Fungal -RiPPs- Like

[sawsanabed]

Hello all,
I am using the antiSMASH V.7 and in this version, there is a new group of RiPPs under the name (Fungal-RiPPs- like). the issue is when I run the big-scape it puts these BGCs into the " other" groups and it does not show it as a RiPPs on the HTML link. Is there any way to overcome this issue

Thanks a lot in advance

[jorgecnavarrom]

Hi
With the upcoming version 2 of BiG-SCAPE, we haven't updated the new detection types from antiSMASH 7. You could manually add this type (fungal-RiPP-like) to the list of RiPPs in the sort_bgc function of the functions.py file (currently here, at line 391, but line number might be different depending on the version you're using):

def sort_bgc(product):
    """Sort BGC by its type. Uses antiSMASH annotations
    (see 
    https://docs.antismash.secondarymetabolites.org/glossary/#cluster-types)
    """
  ...
    ripps_products = {'lantipeptide', 'thiopeptide', 'bacteriocin', 'linaridin', 
                     'cyanobactin', 'glycocin', 'LAP', 'lassopeptide', 
                     'sactipeptide', 'bottromycin', 'head_to_tail', 'microcin', 
                     'microviridin', 'proteusin', 'lanthipeptide', 'lipolanthine', 
                     'RaS-RiPP', 'fungal-RiPP', 'TfuA-related', 'guanidinotides', 
                     'RiPP-like', 'lanthipeptide-class-i', 'lanthipeptide-class-ii', 
                     'lanthipeptide-class-iii', 'lanthipeptide-class-iv',
                     'lanthipeptide-class-v', 'ranthipeptide', 'redox-cofactor',
                     'thioamitides', 'epipeptide', 'cyclic-lactone-autoinducer',
                     'spliceotide', 'RRE-containing', 'crocagin', 'fungal-RiPP-like'}
    saccharide_products = {'amglyccycl', 'oligosaccharide', 'cf_saccharide', 
                     'saccharide'}
...

[lconreur]

Hi,
Different person, same "issue". :) (using Bigscape-1.1.9 I can add 'fungal-RiPP-like' into ripps_products. I guess other categories below can go to 'Others'?

Warning: unknown product 'terpene-precursor'
Warning: unknown product 'NRP-metallophore'
Warning: unknown product 'isocyanide'
Warning: unknown product 'isocyanide-nrp'
Warning: unknown product 'RCDPS'

thank you!

[nlouwen]

Hi!
That would indeed be an option, it mostly depends on which comparisons you would like to make (if you ran with classify). For example, if you would want to compare all NRPS BGCs to the NRP-metallophore, the NRPS category might be better.
Alternatively, you could try BiG-SCAPE version 2, where you can bin directly based on antiSMASH classes or categories (see wiki).

[lconreur]

Thank you, I will go for BiG-SCAPE version 2 :-)

[lconreur]

Hello again (6 months later) !
I'm back on this topic. I am wondering if we could kind of "map" classes or categories to defined bin_labels.
i.e. if I have "other.terpene" as an antismash category and I would like it to be under bin_label "terpene" ? Kind of "personalized bin_label".

My idea behind is to empty bin_label "other". When I look deeper into BGCs, I see I could reclass most of them.

Thank you :)
(I use BiG-SCaPE v2.0.0-beta7)