Computational method for Comparative ReConstruction of genome-scale metabolic networks
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Blast_scripts Import Aug 8, 2013
GTG_scripts Import Aug 8, 2013
Iprscan_scripts Import Aug 8, 2013
data Path fixes Jun 16, 2014
doc Manual Oct 5, 2013
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model_reconstruction_pipeline Re-added missing file Aug 28, 2014
model_training_scripts Import Aug 8, 2013
plotting Import Aug 8, 2013
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MetabolicReconstructionPipeline.py Import Aug 8, 2013
ProjectDir.py Path fixes Jun 16, 2014
README.md Fixed link Mar 23, 2018
ScriptsDir.py Path fixes Jun 16, 2014

README.md

CoReCo

CoReCo is a computational method for reconstructing metabolic networks of multiple species from protein sequence and phylogenetic data.

  1. Software requirements
  2. Data requirements

Software requirements

  1. Python
  2. Perl
  3. InterProScan
  4. NCBI Blast+ toolkit
  5. R
  6. Python module newick
  7. libsbml

Data requirements

  1. UniProt (uniprot_sprot.fasta.gz, uniprot_sport.dat)
  2. EC to GO mapping (ec2go)
  3. KEGG
  4. GTG nrdb40

See doc/CoReCoManual.pdf for installation and usage instructions.

Cite us

  • Pitkänen et al., Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species. PLOS Computational Biology 2014, doi:10.1371/journal.pcbi.1003465
  • Castillo et al., Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction. Biotechnology for Biofuels 2016, doi:10.1186/s13068-016-0665-0