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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

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Computational method for Comparative ReConstruction of genome-scale metabolic networks

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