Pantograph specifications

Information


Unique identifier OMICS_20106
Name Pantograph
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License CeCILL version 2.1
Computer skills Advanced
Version 0.1.1
Stability Stable
Maintained Yes

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Versioning


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Maintainers


  • person_outline anna.zhukova
  • person_outline Nicolas Loira
  • person_outline David Sherman

Publication for Pantograph

Pantograph citations

 (2)
library_books

Analysis of Piscirickettsia salmonis Metabolism Using Genome Scale Reconstruction, Modeling, and Testing

2017
Front Microbiol
PMCID: 5732189
PMID: 29321769
DOI: 10.3389/fmicb.2017.02462

[…] Piscirickettsia salmonis LF-89 metabolic network reconstruction started with the generation of two automatic draft reconstructions. The first draft was created using Pantograph, an orthology-based method that uses as template a metabolic reconstruction of a related organism (). We used Escherichia coli K-12 substr. MG1655 metabolic model iJO1366 () as a template. […]

library_books

Reconstruction of the microalga Nannochloropsis salina genome scale metabolic model with applications to lipid production

2017
BMC Syst Biol
PMCID: 5496344
PMID: 28676050
DOI: 10.1186/s12918-017-0441-1

[…] d literature. First, we searched for orthologs between our N. salina CDS and the C. reinhardtii protein sequences, using Inparanoid [] and OrthoMCL []. Then we built a draft model for N. salina using Pantograph [], taking as a template the iRC1080 model for C. reinhardtii. Then, we looked at the list of genes not present in the draft model, but which annotation included an Enzyme Commission (EC) n […]

Pantograph institution(s)
Center for Mathematical Modeling and Center for Genome Regulation, Universidad de Chile, Santiago, Chile; Inria / Université Bordeaux / CNRS joint project-team MAGNOME, Talence, France
Pantograph funding source(s)
Supported by CONICYT-INRIA, grants from CIRIC-INRIA Chile, Fondap 15090007, Fondecyt 3140480, Basal Grant CMM (UMI-CNRS 2807) and an INRIA CORDIS doctoral fellowship.

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