NAPDOS.UCSD.EDU
NaPDoS | HomeNaPDos Natural Product Domain seeker, a tool for rapid detection and analysis of secondary metabolite genes
http://napdos.ucsd.edu/
NaPDos Natural Product Domain seeker, a tool for rapid detection and analysis of secondary metabolite genes
http://napdos.ucsd.edu/
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NaPDoS | Home | napdos.ucsd.edu Reviews
https://napdos.ucsd.edu
NaPDos Natural Product Domain seeker, a tool for rapid detection and analysis of secondary metabolite genes
napdos.ucsd.edu
NaPDoS | Overview
http://napdos.ucsd.edu/background.html
Natural Product Domain Seeker. Traditional methods have shown that nature can provide many surprising new compounds, yet even well known organisms can harbor cryptic gene clusters for which the chemical products have yet to be discovered (2). Increasing numbers of fully sequenced genomes, along with improved understanding of the genetics and enzymology of secondary metabolism, present an opportunity to enhance natural product discovery through systematic bioinformatic data analysis. Domain-specific phylo...
NaPDoS | Tutorial
http://napdos.ucsd.edu/tutorial.html
Natural Product Domain Seeker. The NaPDoS bioinformatic pipeline is shown in the following diagram. The web interface to this pipeline is divided into five consecutive steps. Click on the link for each step to get detailed instructions. HMM search (Genomic data only). Begin NaPDoS analysis by selecting a domain type. Select a query type (protein, predicted coding sequence, PCR product, genomic, or metagenomic). If you would like to analyze larger data sets. Default parameter settings are recommended for ...
NaPDoS | Pathways
http://napdos.ucsd.edu/pathways.html
Natural Product Domain Seeker. The NaPDoS reference database currently covers 96 different PKS, NRPS, and hybrid pathways with chemically characterized products, including 648 manually curated, trimmed amino acid sequences for KS and C domains. Links to reference sequences in fasta format and a tab-delimited version of this table are available for DOWNLOAD. Actinorh NP 629237 KSa. Actinorh NP 629238 KSb. HSAF (heat stable antifungal factor). Strep ZP 06279092 i. Yersi YP 070123 H.
NaPDoS | Run Analysis
http://napdos.ucsd.edu/run_analysis.html
Natural Product Domain Seeker. Choose a domain and query type, then enter your data to identify candidate KS and/or C domains. Can be used to customize program parameters. Predicted protein sequences (amino acid). Predicted coding sequences or PCR products (DNA). Genome or metagenome contigs (DNA). Enter or paste sequence(s) in FASTA. Max db hits per domain.
NaPDoS | Home
http://napdos.ucsd.edu/napdos_home.html
Natural Product Domain Seeker. Natural Product Domain Seeker. NaPDos is a bioinformatic tool for the rapid detection and analysis of secondary metabolite genes. This tool is designed to detect and extract C- and KS- domains from DNA or amino acid sequence data, including PCR amplicon products, individual genes, whole genomes, and metagenomic data sets. PLoS One. 2012;7(3):e34064 Epub 2012 Mar 29. PubMed PMID: 22479523.
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Current projects - Allen Lab
http://microbialoceans.ucsd.edu/projects
Marine Microbial HOC Genomics. Halogenated organic compounds (HOCs)are widely distributed among organisms occupying higher trophic levels of the marine food web. Chemical analysis of environmental and biological samples have shown that these HOCs originate from both natural and anthropogenic sources, but in most cases their precise species of origin and food web entry points are unknown. As members of the Scripps Center for Oceans and Human Health. Within microbial genomes and metagenomes.
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NaPDoS | Home
Natural Product Domain Seeker. Natural Product Domain Seeker. NaPDos is a bioinformatic tool for the rapid detection and analysis of secondary metabolite genes. This tool is designed to detect and extract C- and KS- domains from DNA or amino acid sequence data, including PCR amplicon products, individual genes, whole genomes, and metagenomic data sets. PLoS One. 2012;7(3):e34064 Epub 2012 Mar 29. PubMed PMID: 22479523.
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