Table 5.
Bioinformatic tools and databases for SM study
| S. no. | Name | Functions | URL | References |
|---|---|---|---|---|
| 1. | Secondary Metabolite Bioinformatics Portal (SMBP) | Database catalog and links of bioinformatic tool for the secondary metabolite study | http://www.secondarymetabolites.org | Palazzotto and Weber (2018) |
| 2. | Antibiotics and Secondary Metabolite Analysis SHell (antiSMASH) | Web application and autonomous tool (LINUX, MacOS and MS Windows) to mine and analyze BGCs; include genomic tools and a homology-based metabolic modeling pipeline | http://antismash.secondarymetabolites.org. | Blin et al. (2013) |
| 3. | Natural Product Domain Seeker (NaPDoS) | Tool for the rapid detection and analysis of secondary metabolite genes to detect and classify KS and C domains | http://napdos.ucsd.edu/run_analysis.html | Ziemert et al. (2012) |
| 4. | NP.searcher | Web application search tool (LINUX) to mine for PKS/NRPS BGCs | http://dna.sherman.lsi.umich.edu/ | Chavali and Rhee (2018) |
| 5. | Genes to natural products/prediction informatics for secondary metabolomes (GNP/PRISM) | Cluster mining tool and analyze the pathway for PKS and NRPS | Skinnider et al. (2017) | |
| 6. | Secondary Metabolite Unknown Region Finder (SMURF) | Tool to mine PKS/NRPS/terpenoid gene clusters in fungal genome | www.jcvi.org/smurf/ | Wang et al. (2016) |
| 7. | Cluster Finder | Stand-alone tool (LINUX and MacOS) to detect BGCs with secondary metabolite gene clusters in genomic and metagenomic data | https://github.com/petercim/ClusterFinder | Chavali and Rhee (2018) |
| 8. | HMMER web server | Identify ketosynthase domain and condensation domain encoding genes in genomic and metagenomic datasets | http://hmmer.org/ | Potter et al. (2018) |
| 9. | XCMS | Metabolomic data processing algorithm tool to extract metabolic features from raw MS data and perform statistical analysis. | https://xcmsonline.scripps.edu. | Domingo-Almenara et al. (2018) |
| 10. | iSNAP | Web tool which automatically identify metabolites in MS/MS data based on genomic data | http://snap.cifr.ncsu.edu | Baptista et al. (2022) |
| 11. | CLUsterSEquenceANalyzer (CLUSEAN) | Web accessible database of PKS/NRPS BGCs and annotation pipeline for secondary metabolite biosynthetic gene clusters. | Chavali and Rhee (2018) | |
| 12. | Minimum Information about a Biosynthetic Gene cluster (MIBiG) | Web tool for annotations and metadata on biosynthetic gene clusters and their molecular products. | https://mibig.secondarymetabolites.org/ | Bian et al. (2020) |
| 13. | EvoMining approach | Stand-alone tool for phylogenomic approach of cluster identification | (https://github.com/nselem/evomining/wiki) | Sélem-Mojica et al. (2019) |
| 14. | Integrative meta-analysis of expression data (INMEX) | Web-based tool to support meta-analysis of multiple gene expression datasets | http://www.inmex.ca | Xia et al. (2013) |
| 15. | Metscape 2 | Web tool for the analysis and visualization of metabolomics and gene expression data and visualize changes in the gene/metabolite data. | http://metscape.ncibi.org | Rosato et al. (2018) |
| 16. | Crux | MS analysis toolkit that combine computational, machine learning and statistical methods for proteomics analysis | https://crux.ms/ | McIlwain et al. (2014) |