Skip to content

GitLab

  • Projects
  • Groups
  • Snippets
  • Help
    • Loading...
  • Help
    • Help
    • Support
    • Community forum
    • Submit feedback
    • Contribute to GitLab
  • Sign in
BiG-SCAPE
BiG-SCAPE
  • Project overview
    • Project overview
    • Details
    • Activity
    • Releases
  • Repository
    • Repository
    • Files
    • Commits
    • Branches
    • Tags
    • Contributors
    • Graph
    • Compare
  • Issues 6
    • Issues 6
    • List
    • Boards
    • Labels
    • Service Desk
    • Milestones
  • Merge Requests 0
    • Merge Requests 0
  • CI / CD
    • CI / CD
    • Pipelines
    • Jobs
    • Schedules
  • Operations
    • Operations
    • Incidents
    • Environments
  • Packages & Registries
    • Packages & Registries
    • Container Registry
  • Analytics
    • Analytics
    • CI / CD
    • Repository
    • Value Stream
  • Wiki
    • Wiki
  • Members
    • Members
  • Collapse sidebar
  • Activity
  • Graph
  • Create a new issue
  • Jobs
  • Commits
  • Issue Boards
  • medema-group
  • BiG-SCAPEBiG-SCAPE
  • Wiki
  • big scape classes

Last edited by Jorge Navarro Jun 07, 2019
Page history

big scape classes

BiG-SCAPE classes

By default, BiG-SCAPE will try to separate clusters into eight classes. This is done based on the product annotation from antiSMASH. New labels introduced in antiSMASH 5 are annotated with a superscript '5'.

The rules followed are currently:

antiSMASH annotation BiG-SCAPE class
t1pks, T1PKS^5 PKS I
transatpks, t2pks, t3pks, otherks, hglks, transAT-PKS^5, transAT-PKS-like^5, T2PKS^5, T3PKS^5, PKS-like^5, hglE-KS^5 and combinations of these with {t1pks, T1PKS^5} or themselves PKS other
nrps, NRPS^5, NRPS-like^5, thioamide-NRP^5 NRPS
lantipeptide, thiopeptide, bacteriocin, linaridin, cyanobactin, glycocin, LAP, lassopeptide, sactipeptide, bottromycin, head_to_tail, microcin, microviridin, proteusin, lanthipeptide^5, lipolanthine^5, RaS-RiPP^5, fungal-RiPP^5 and combinations of these RiPPs
amglyccycl, oligosaccharide, cf_saccharide, saccharide^5 and combinations of these Saccharides
terpene Terpene
any of {t1pks, T1PKS^5, transatpks, t2pks, t3pks, otherks, hglks, transAT-PKS^5, T2PKS^5, T3PKS^5, PKS-like^5, hglE-KS^5} + any of {nrps, NRPS^5, NRPS-like^5, thioamide-NRP^5} PKS/NRPS Hybrids
acyl_amino_acids, arylpolyene, aminocoumarin, ectoine, butyrolactone, nucleoside, melanin, phosphoglycolipid, phenazine, phosphonate, other, cf_putative, resorcinol, indole, ladderane, PUFA, furan, hserlactone, fused, cf_fatty_acid, siderophore, blactam, fatty_acid^5, PpyS-KS^5, CDPS^5, betalactone^5, PBDE^5, tropodithietic-acid^5, NAGGN^5, halogenated^5 and any combined annotation Others
* < mix >

Hybrids

If the hybrids mode is enabled, some clusters could be analyzed in different classes (if those are valid classes):

If cluster is the PKS-NRP_Hybrids BiG-SCAPE class: the cluster will also be put in the NRPS class and one of the PKS classes (PKS I or PKS other). If the cluster contains the t1pks annotation, it will always be put on the PKS I class.

If the cluster is classified as Others and BiG-SCAPE detects that it's because of a multiple annotation (e.g. terpene-t1pks), BiG-SCAPE will also put the cluster in every different individual class.

Clone repository
  • Alignment Modes
  • GCFs and GCCs
  • anchor file
  • big scape classes
  • domain prediction
  • Home
  • input
  • installation
  • output
  • parameters