NP.searcher statistics

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NP.searcher specifications

Information


Unique identifier OMICS_09246
Name NP.searcher
Alternative name Natural products search engine
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data DNA sequence
Input format FASTA
Output data Simplified Molecular Input Line Entry Specifications (SMILES) of the predicted possible polyketide and nonribosomal peptide natural products
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline David H. Sherman <>

Information


Unique identifier OMICS_09246
Name NP.searcher
Alternative name Natural products search engine
Interface Web user interface
Restrictions to use None
Input data DNA sequence
Input format FASTA
Output data Simplified Molecular Input Line Entry Specifications (SMILES) of the predicted possible polyketide and nonribosomal peptide natural products
Programming languages C++
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline David H. Sherman <>

Publication for Natural products search engine

NP.searcher in publications

 (9)
PMCID: 5702503
PMID: 29209209
DOI: 10.3389/fphar.2017.00828

[…] these tools are generally divided into two categories: high-confidence/low-novelty and low-confidence/high-novelty. high-confidence/low-novelty includes tools such as clusean13, clustscan14, np.searcher15, smurf16 and antismash (medema et al., ). these tools analyze hidden markov models (hmms) with manually curated cutoffs to identify signature genes or domains that are highly specific […]

PMCID: 5658590
PMID: 29076296
DOI: 10.1111/1751-7915.12882

[…] a comprehensive web server and a stand‐alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters of any type, with other more specific tools such as clustscan, np.searcher or sbspks focusing on non‐ribosomal peptide and polyketide biosynthesis pathways. such bioinformatic tools are creating great expectations for future drug discovery by revealing […]

PMCID: 5541019
PMID: 28824571
DOI: 10.3389/fmicb.2017.01438

[…] bioinformatic tools designed for the identification of clusters involved in secondary metabolism such as prism (skinnider et al., ), antismash 3.0 (weber et al., ), napdos (ziemert et al., ), np.searcher (li et al., ), and the bacteriocin specific software bagel3 (van heel et al., ) and the b. amyloliquefaciens genomes available in databases, we documented high structural and functional […]

PMCID: 4849084
PMID: 27092515
DOI: 10.3390/md14040080

[…] predictive models. in the case of pks, substrate redundancy makes reliable prediction somewhat more challenging []. nevertheless, refined predictive models were incorporated in antismash, and np.searcher [] as well as in more specific tools like nrpspredictor2 (nrps.informatik.uni-tuebingen.de) [], sbspks (http://www.nii.ac.in/~pksdb/sbspks/master.html) [] and nrps-pks-substrate-predictor […]

PMCID: 4673338
PMID: 26697425
DOI: 10.3389/fbioe.2015.00199

[…] bgcs is nowadays possible within a few of hours., continuous progress has enabled the emergence of bioinformatics platforms, such as clusean (weber et al., ), clustscan (starcevic et al., ), np.searcher (li et al., ), smurf (khaldi et al., ), and antismash (medema et al., ; blin et al., ; weber et al., ). the latter is the most popular system for automated bnp genome mining since […]


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NP.searcher institution(s)
Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA; Departments of Chemistry, and Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA

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