. 2019 Mar 12;103(8):3277–3287. doi: 10.1007/s00253-019-09708-z

Table 1.

Computational programs for secondary metabolite gene mining

Category	Software	Year/version	Features	User interface	Computation platform	Target organism(s)	Reference(s)
BGC prediction	BAGEL	2006/v1, 2010/v2, 2013/v3	Identify bacteriocins and RiPPs using HMM search with bacteriocin database	Web	Server	Bacteria	(de Jong et al. 2010, 2006; van Heel et al. 2013)
	ClustScan	2008	Identify BGCs using HMM search and predict product structure	GUI	Local PC	Bacteria	(Starcevic et al. 2008)
	NP.searcher	2009	Identify BGCs using BLAST and construct the structure of natural products	Web/command line	Server/local PC	Bacteria	(Li et al. 2009)
	SMURF	2010	Predict secondary metabolite biosynthesis gene clusters based on their genomic context and domain content using HMM search	Web	Server	Fungi	(Khaldi et al. 2010)
	antiSMASH	2011/v1, 2013/v2, 2015/v3, 2017/v4	Identify BGCs using HMMer3 to search experimentally characterized signature proteins	Web/command line	Server/local PC	Bacteria, fungi, plants	(Blin et al. 2013, 2017; Medema et al. 2011; Weber et al. 2015)
	ClusterFinder	2014	Identify BGCs using a hidden Markov model-based probabilistic algorithm	Command line	Local PC	Bacteria	(Cimermancic et al. 2014)
	PRISM	2015/PRISM,2016/RiPP-PRISM,2017/PRISM3	Identify BGCs using BLAST and HMMER and structure prediction using HMM	Web	Server	Bacteria	(Skinnider et al. 2015, 2016, 2017)
	EvoMining	2016	Identify BGCs using phylogenomic analysis	Command line	Local PC	Actinobacteria	(Cruz-Morales et al. 2016)
	RODEO	2017	Identify BGC and RiPP precursor peptide using HMM and machine learning	Web	Server	Bacteria	(Tietz et al. 2017)
	ARTS	2017	Uses three additional selection criteria, including BGC proximity, gene duplication and horizontal gene transfer, to prioritize antiSMASH-detected BGCs	Web	Server	Bacteria	(Alanjary et al. 2017)
Biosynthetic gene analysis	SBSPKS	2010	Analyze the 3D structure of PKS protein using BLAST and SCWRL; predict the order of substrate channeling between multiple ORFs in a modular PKS cluster based on docking domain interaction	Web	Server	Bacteria, fungi, plants	(Anand et al. 2010)
Biosynthetic gene analysis	NaPDoS	2012	Predict natural products of secondary metabolite genes using BLAST and domain phylogeny	Web	Server	Bacteria	(Ziemert et al. 2012)