Gapseq Versions Save

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks


1 year ago

  • Improvement of reaction and metabolite database for archaeal metabolism (incl. methanogenesis, mevalonate pathways, chorismate biosynthesis)
  • Anaerobic Degradation pathways for secondary plant metabolites (incl. daidzin, daidzein, quercetin, genistein, sulfoquinovose)
  • New module for automated prediction of gapfill-/growth- medium
  • Improved performance of SBML export
  • gapseq version tags in main output files
  • Improved prediction of reactions with multiple associated EC-numbers
  • Revised reaction and metabolite database for C1-metabolism (i.e. Wood-Ljungdahl pathway)
  • improved representation of nitrogen metabolism (e.g. ammonia oxidation)
  • new bile acids pathways (deamination, 7dehydroxylation, epimerization)
  • easier installation via conda libsbml package
  • support to adjust for environmental conditions (low/high h2)
  • enabled support for photosynthesis
  • full model construction on the fly
  • xylan degradation
  • medium prediction
  • improved threonine biosynthesis prediction
  • updated reaction sequences (uniprot) and pathway databases (metacyc)
  • revised transporter prediction
  • extended nucleotide metabolism
  • updated archaeal pathways


2 years ago

A man may fish with the worm that hath eat of a king, and eat of the fish that hath fed of that worm ... a king may go a progress through the guts of a beggar (Hamlet: act 4, scene 3)

  • archaea support (especially methanogens)
  • new documentation
  • improved fiber degradation
  • extended electron bifurcation reactions
  • improved anaerobic vitamine biosynthesis
  • more cases of extracellular degradation
  • added 'gapseq adapt' to manually improve models
  • enabled photosynthesis
  • many smaller bugfixes


3 years ago

  • official productive release
  • used for results in the gapseq manuscript


4 years ago

  • draft model generation
  • enzyme complex detection
  • gapfilling by bitscore weight


4 years ago

Preliminary release used in first studies

  • pathway analysis for metacyc, kegg, seed, and custom pathways
  • gapfilling of metabolic models
  • draft model creation
  • a lot of corrections in seed reaction database
  • transporter prediction