NaPDoS statistics

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Associated diseases

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NaPDoS specifications

Information


Unique identifier OMICS_18271
Name NaPDoS
Interface Web user interface
Restrictions to use None
Input data Some protein sequences (amino acid).
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Paul Jensen <>

Additional information


http://napdos.ucsd.edu/tutorial.html

Publication for NaPDoS

NaPDoS in publications

 (36)
PMCID: 5878181
PMID: 29602945
DOI: 10.1038/s41467-018-03690-2

[…] to cure the strain from plasmid pbbr5-flp. mutations in hamc, hamd, hame, and afca were generated by the aid of the frt/flp system., protein domains were analyzed with the nrps/pks analysis tool, napdos (natural product domain seeker) and the interproscan 5 online tool., the architecture search mode of the multigeneblast software was used to identify gene clusters similar to the ham cluster […]

PMCID: 5826242
PMID: 29515540
DOI: 10.3389/fmicb.2018.00251

[…] for accurate metagenome binning. these genomes were screened for secondary metabolism genes, such as polyketide synthases (pks) and non-ribosomal peptide synthases (nrps), using the anti-smash and napdos workflows. with this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. a total of 18 nrps, 19 pks, and 3 hybrid pks/nrps […]

PMCID: 5754493
PMID: 29301884
DOI: 10.1128/genomeA.01404-17

[…] revealed one known secondary metabolite cluster, an ectoine. this is a natural compound used by the microorganism to survive in osmotic stress and found mainly in halophilic bacteria (, ). the napdos () analysis revealed four gene clusters related to the ketosynthase domain, three gene clusters related to fatty acid synthesis, and one gene cluster related to a spinosad. this cluster […]

PMCID: 5738826
PMID: 29276571
DOI: 10.1186/s40793-017-0303-x

[…] to explore potential production of secondary metabolites of 10.1601/nm.17912 genome. in addition, we developed a bioinformatics workflow which included platforms such as antismash [], bagel3 [] and napdos []., the genome of 10.1601/nm.17912 is 2.68 mbp with a 53.7% gc content. a total of 2609 genes were predicted and of those, 2543 were protein coding genes and 66 were rna genes. the properties […]

PMCID: 5731063
PMID: 29255573
DOI: 10.1186/s40793-017-0292-9

[…] gene prediction analysis and functional annotation was performed within the integrated microbial genomes (img-er) []., biosynthetic clusters were predicted running antismash [], bagel3 [] and napdos []. antismash was run using the genbank file generated during annotation from the img-er as the input. before running the antismash server tool, clusterfinder algorithm [], whole-genome pfam […]


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NaPDoS institution(s)
Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA; Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, CA, USA; Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
NaPDoS funding source(s)
Supported by the National Institutes of Health grant numbers RO1GM086261, UO1TW0007401, and RO1GM085770, and a grant from the German Research Foundation (DFG 1325/1-1).

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