Pancoregen protocols

View Pancoregen computational protocol

Pancoregen statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Protein-coding gene prediction chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Pancoregen specifications

Information


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

Download


Versioning


Add your version

Maintainers


  • 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

2018
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, […]


To access a full list of citations, you will need to upgrade to our premium service.

Pancoregen in publications

 (2)
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 […]


To access a full list of publications, you will need to upgrade to our premium service.

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).

Pancoregen reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Pancoregen