Important notes#

This release increases the minimum python version to 3.9.

New features#

Minor#

Detection Rules

  • Added rules for darobactin, highly reducing type II PKS, hydrogen cyanide, isocyanide, rSAM-related archaeal RiPPs, triceptide
  • Added support for "extender" conditions to rules, for cases where a continguous section of some core genes might be too far from the other core genes to be properly marked
  • Added extenders to trans-AT PKS rule to mark all genes in long chains of trans-AT modules as core
  • Changed rule categories for larylpolyenes and PUFAs
  • Changed ladderane rule to be more specific
  • Changed the neighbourhood range of NI-siderophores to be wider in order to cover all of the known clusters

Additionally, new command line options are available to limit detected cluster types to a subset:

  • --hmmdetection-limit-to-rule-names: restricts protoclusters detected to the named types
  • --hmmdetection-limit-to-rule-categories: restricts protoclusters detected to the named categories

Input handling

  • Added support for reusing JSON results compressed with bzip2

Analysis

  • Updated PFam reference database from 34.0 to 35.0
  • Updated GO mappings to 2023-07-05 release
  • Updated ClusterBlast reference data from antiSMASH-database version 3.0 to 4.0
  • Updated CompaRiPPson reference data from antiSMASH-database version 3.0 to 4.0

Output

  • Added the product category of protoclusters to their relevant section in JSON results
  • Added clusterblast similarity percentage to JSON results
  • Removed raw ClusterBlast result file due to size and lack of clarity

Visualisation

  • Added a link to CDS details that allows BLAST searches against the antiSMASH-database
  • Added download link for JSON results file
  • Added record versions, where available, to record identifiers in HTML results
  • Removed NCBI genomic context links by default, these can be explicitly re-enabled with --html-ncbi-context
  • Removed links to the now-defunct SEARCHGTr webservice
  • Changed lasso peptide and sactipeptide core colouring to only cover cysteines in HTML results
  • Changed CompaRiPPson characters in consensus to use the same colouring as in the queries, where relevant

Fixes and small changes#

Input handling

  • Changed all generated CDS translations to start with methionine, even when using an alternative start codon

Analysis

  • Removed some rare instances of fused lanthipeptide genes being interpreted as a precursors
  • Changed lasso peptide precursor handling to avoid motif duplication when shared by two protoclusters
  • Changed trans-AT PKS module classification to be less strict
  • Changed lanthipeptide tailoring enzyme detection to be less strict
  • Changed all RiPP precursor ORF finding to be less strict
  • Changed capreomycidine substrate SMILES to reorder the backbone

Output

  • Added error output to log files, when relevant

Visualisation

  • Changed default ClusterCompare comparison mode shown from ProtoclusterToRegion to RegionToRegion

Numerous other small changes and fixes were made internally, for a full list see the git shortlog.