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The Natural Product Domain Seeker NaPDoS: A Phylogeny Based Bioinformatic Tool to Classify Secondary Metabolite Gene Diversity

Figure 1

NaPDoS bioinformatic pipeline.

The web interface to this pipeline is divided 3 consecutive steps. Nucleic acid sequences are translated into predicted amino acids and genomic sequences are screened using Hidden Markov Models (HMM). For protein and small nucleic acid sequences a BLAST search is performed against curated reference database examples to identify matches to known PKS/NRPS pathways. Selected candidate sequences plus the BLAST results are trimmed and inserted into a manually curated reference alignment, keeping the original reference alignment intact. This alignment is used to build a tree.

Figure 1

doi: https://doi.org/10.1371/journal.pone.0034064.g001