Pancoregen protocols

View Pancoregen computational protocol

Pancoregen statistics

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Citations per year

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Associated diseases

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Pancoregen specifications


Unique identifier OMICS_22335
Name Pancoregen
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Sandip Paul <>
  • person_outline Archana Bhardwaj <>
  • person_outline Sumit Bag <>
  • person_outline Evgeni Sokurenko <>
  • person_outline Sujay Chattopadhyay <>

Publication for Pancoregen

Pancoregen in pipeline

PMCID: 5867892
PMID: 29558450
DOI: 10.3390/genes9030171

[…] onto an initial seed genome. genbank files for three reference strains (f2365 seed genome, clip80459 and egd-e) were compared with the clinical and food/food processing environment isolates., pancoregen [] was subsequently used to construct the pan-genomic database of orthogolous genes using the clinical and food associated isolates along with suitable references including f2365, […]

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Pancoregen in publications

PMCID: 5867892
PMID: 29558450
DOI: 10.3390/genes9030171

[…] that there are an average of 2900 genes per strain and approximately 2400 of these genes are part of the core genome (≈80%). a pan-genomic database of orthogolous genes was constructed using pancoregen []. a cut-off of 80% for sequence identity and gene length coverage resulted in a total of 3105 orthologous genes amongst the genome sequences analysed. the observed core genome shared […]

PMCID: 4864206
PMID: 27167125
DOI: 10.1371/journal.pntd.0004712

[…] annotated kc583 genome as a reference. the protein-coding genes of these draft genomes were then annotated using a combination of the rast annotation server [] and our recently developed software, pancoregen []. using pancoregen, we constructed the pan-genomic profile at different nucleotide sequence identity threshold values (75%, 80%, 85%, 90% and 95%) keeping a constant 95% threshold […]

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Pancoregen institution(s)
Department of Microbiology, University of Washington, Seattle, WA USA; CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, India
Pancoregen funding source(s)
Supported by the National Institutes of Health (grant no. R01AI106007).

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