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CoReCo specifications


Unique identifier OMICS_20084
Name CoReCo
Alternative name Comparative ReConstruction
Software type Framework/Library, Package/Module, Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A set of protein coding sequences for each species.
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, R
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Esa Pitkanen

Additional information

Publication for Comparative ReConstruction

CoReCo citations


N acetylcysteine Counteracts Adipose Tissue Macrophage Infiltration and Insulin Resistance Elicited by Advanced Glycated Albumin in Healthy Rats

Front Physiol
PMCID: 5616024
PMID: 29018354
DOI: 10.3389/fphys.2017.00723

[…] Olympus camera (Olympus Co, St Laurent, Quebec, Canada) coupled to an Olympus microscope (Olympus BX51), from which the images were sent to an LG monitor by means of a digitizing system (Oculus TCX, Coreco, Inc, St. Laurent, Quebec, Canada) and downloaded to a computer (Pentium 1330 Mhz). The number of inflammatory cells and F4/80-positive macrophages in periepididymal adipose tissue (along with […]


Genetic engineering of Trichoderma reesei cellulases and their production

PMCID: 5658622
PMID: 28557371
DOI: 10.1111/1751-7915.12726

[…] as the use of whole‐cell metabolic models, likely offer the best available strategy for the identification of the limiting steps for cellulase production. To this end, Castillo et al. () applied the CoReCo (comparative metabolic reconstruction framework) pipeline (Pitkänen et al., ) for the construction of a high‐quality metabolic model of T. reesei (BIOMODELS database). The model contains a biom […]


Whole genome metabolic model of Trichoderma reesei built by comparative reconstruction

Biotechnol Biofuels
PMCID: 5117618
PMID: 27895706
DOI: 10.1186/s13068-016-0665-0

[…] Instead of the actual genomes of the input organisms, CoReCo uses the full set of protein sequences from each organism. In each case, the protein sequence data for the species of interest were downloaded from JGI and the FASTA headers modified to have a […]


Machine Learning of Protein Interactions in Fungal Secretory Pathways

PLoS One
PMCID: 4956264
PMID: 27441920
DOI: 10.1371/journal.pone.0159302

[…] ic biological networks i.e. metabolic pathways depending on what type of training labels are used. Our method uses as features various sequence similarity and protein family analysis derived from the CoReCo pipeline []. Although our method relies partly on sequence similarity, it is, through a combination of methods, still able to predict for proteins that do not belong into any known protein fami […]


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CoReCo institution(s)
Department of Computer Science, University of Helsinki, Helsinki, Finland; Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland; VTT Technical Research Centre of Finland, Espoo, Finland; Department of Information and Computer Science, Aalto University, Espoo, Finland; Institute of Biotechnology & Department of Biosciences, University of Helsinki, Helsinki, Finland
CoReCo funding source(s)
Supported by Academy of Finland postdoctoral researcher’s fellowships (grant no 127715 and 140380), and supported in part by the EU FP7 grants BIOLEDGE (FP7-KBBE-289126) and PASCAL2 (ICT-2007-216886), Ministry of Employment and the Economy KYT programme (GEOBIOINFO, grant 26/2011/KYT), Academy of Finland grant 118653 (ALGODAN), and Finnish Centre of Excellence in White Biotechnology - Green Chemistry, Project No. 118573.

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