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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 citations

 (42)
library_books

Biosynthesis of fragin is controlled by a novel quorum sensing signal

2018
Nat Commun
PMCID: 5878181
PMID: 29602945
DOI: 10.1038/s41467-018-03690-2

[…] 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 in o […]

library_books

Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome Resolved Metagenomics

2018
Front Microbiol
PMCID: 5826242
PMID: 29515540
DOI: 10.3389/fmicb.2018.00251

[…] . Five PKS domains were retrieved, including the minimal core from one of the ORFs on this contig. The KS domain BLASTP result shows 82% (and 99% coverage) similarity with Mycobacterium kansasii. The NAPDOS analysis from the KS domain suggests that it could be a modular (epothilone pathway) or iterative type I PKS similar to the calicheamicin pathway. However, by using the phylogenetic analysis it […]

library_books

Draft Genome Sequence of Marinobacter sp. Strain ANT_B65, Isolated from Antarctic Marine Sponge

2018
Genome Announc
PMCID: 5754493
PMID: 29301884
DOI: 10.1128/genomeA.01404-17

[…] alysis 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 was ass […]

library_books

Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring

2017
Stand Genomic Sci
PMCID: 5738826
PMID: 29276571
DOI: 10.1186/s40793-017-0303-x

[…] g 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 []. […]

library_books

Draft genome sequence of Pseudomonas extremaustralis strain USBA GBX 515 isolated from Superparamo soil samples in Colombian Andes

2017
Stand Genomic Sci
PMCID: 5731063
PMID: 29255573
DOI: 10.1186/s40793-017-0292-9

[…] le-genome PFAM analysis [] and Enzyme Commission (EC) number prediction were selected. BAGEL3 is a tool specialized in predicting RiPPs and Bacteriocins using as FASTA file as the input. Finally, the NaPDoS tool was run four times per genome; first with a FASTA nucleotide file as the input and seeking KS domains and second with the same input but seeking C domains. The third and fourth runs were w […]

library_books

Genomic features of “Candidatus Venteria ishoeyi”, a new sulfur oxidizing macrobacterium from the Humboldt Sulfuretum off Chile

2017
PLoS One
PMCID: 5728499
PMID: 29236755
DOI: 10.1371/journal.pone.0188371

[…] TP searches using non redundant databases. Also, to explore the presence of gene clusters involved in biosynthesis of secondary metabolites, the antiSMASH stand-alone software version 3.0 [–] and the NapDos platform [] to detect C- and KS- domains, were used. Additionally, the identification of CRISPR repeats was carried out by the CRISPRFinder tool []. The assembly visualization was made with the […]

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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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