UPGRADE NOTICE:

This version of NaPDoS has been superceded by a newer version called NaPDoS2. We highly recommend that you switch to the new version, which is faster, more accurate, and includes a wider range of reference products:

https://npdomainseeker.sdsc.edu/napdos2

A complete description of the upgrade is provided in the following publication:

Klau LJ, Podell S, Creamer KE, Demko AM, Singh HW, Allen E, Moore BS, Ziemert N, Letzel AC, Jensen PR. The Natural Product Domain Seeker version 2 (NaPDoS2) webtool relates ketosynthase phylogeny to biosynthetic function.Journal of Biological Chemistry, 2022, 102480, ISSN 0021-9258, https://doi.org/10.1016/j.jbc.2022.102480.

 

 

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.

Candidate secondary metabolite domains are identified by sequence comparison to a broad set of manually curated reference genes from well-characterized chemical pathways. Candidate gene sequences are extracted, trimmed, translated (if necessary) and subjected to domain-specific phylogenetic clustering to predict what their putative products might be, and to determine whether these products are likely to produce compounds similar to or different from previously known biosynthetic pathways. If you find this tool helpful, please cite the reference below.

workflow_diagram

Reference

Ziemert N, Podell S, Penn K, Badger JH, Allen E, Jensen PR The Natural Product Domain Seeker NaPDoS: A Phylogeny Based Bioinformatic Tool to Classify Secondary Metabolite Gene Diversity. PLoS One. 2012;7(3):e34064 Epub 2012 Mar 29. PubMed PMID: 22479523