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PanFP specifications

Information


Unique identifier OMICS_10240
Name PanFP
Alternative name Pangenome-based Functional Profiles
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Andrey A. Gorin

Publication for Pangenome-based Functional Profiles

PanFP citations

 (5)
library_books

Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen fixing rhizobium symbioses

2018
Proc Natl Acad Sci U S A
PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115

[…] nd Parasponia (). In contrast to NFP1, NFP2 is consistently pseudogenized in Trema species ( and SI Appendix, Figs. S22 and S23). In an earlier study, we used RNAi to target PanNFP1 (previously named PaNFP), which led to reduced nodule numbers and a block of intracellular infection by rhizobia as well as arbuscular mycorrhiza (). However, we cannot rule out that the RNAi construct unintentionally […]

library_books

The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder

2017
Mov Disord
PMCID: 5811909
PMID: 28843021
DOI: 10.1002/mds.27105

[…] (ANCOM) analysis was performed using the R (R Foundation for Statistical Computing) implementation. Functional community profiles were predicted based on classified OTU abundances postfiltering using PanFP, and differential analysis was carried out on sum‐normalized data sets using the Mann‐Whitney U test. All P values, except those used for the detection of potential confounders, were adjusted fo […]

library_books

Bacterial‐induced calcium oscillations are common to nitrogen‐fixing associations of nodulating legumes and non‐legumes

2015
New Phytol
PMCID: 4736677
PMID: 26010117
DOI: 10.1111/nph.13464

[…] nd to NGR234 Nod factor may have evolved very recently and could have faciliated the emergence of nodulation in P. andersonii. Molecular studies have revealed that the same receptor in P. andersonii, PaNFP, is involved in the recognition of symbiotic signalling molecules from both AM fungi and rhizobial bacteria (Op den Camp et al., ). Possibly a minor difference within the receptor between Trema […]

library_books

Interaction of Medicago truncatula Lysin Motif Receptor Like Kinases, NFP and LYK3, Produced in Nicotiana benthamiana Induces Defence Like Responses

2013
PLoS One
PMCID: 3672211
PMID: 23750228
DOI: 10.1371/journal.pone.0065055

[…] P functions in these processes alone or in co-operation with (an)other RLK(s).LysM-RLKs in non-legume species also govern plant-microbe interactions. An MtNFP/LjNFR5 homolog in Parasponia andersonii, PaNFP, is involved in interactions with Sinorhizobium sp. NGR234 and Rhizophagus irregularis (formerly Glomus intraradices), resulting in nitrogen-fixing and arbuscular mycorrhiza symbiosis, respectiv […]

library_books

Heart of Endosymbioses: Transcriptomics Reveals a Conserved Genetic Program among Arbuscular Mycorrhizal, Actinorhizal and Legume Rhizobial Symbioses

2012
PLoS One
PMCID: 3435296
PMID: 22970303
DOI: 10.1371/journal.pone.0044742

[…] ases may be responsible for selective processing of substrates present in the peri-fungal space, generating peptides recognised by leucine-rich repeat receptors involved in the AM interaction such as PaNFP or SYMRK. Interestingly, a gene encoding a putative receptor with LRR repeats (CG-R02f_036_O05) was induced in AM in all three plants. Proteases may also be involved in the cell wall loosening a […]

Citations

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PanFP institution(s)
Comparative Genomics Group, Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Joint Institute for Computational Sciences, University of Tennessee, Knoxville, TN, USA; Systems Genetics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Fish, Wildlife and Conservation Biology, Colorado State University, Fort Collins, CO, USA; Department of Microbiology, University of Tennessee, Knoxville, TN, USA; Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA

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