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User:AndyT

Matt Hutchings — Tue, 20 Oct 2026 16:05:35 GMT

User account AndyT was created by Matt Hutchings

Bioinformatics

Matt Hutchings — Mon, 19 Oct 2026 14:45:47 GMT

2026 SSAMM - Bioinformatics Tools and Online Resources

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	===~~2024~~ SSAMM - Bioinformatics Tools and Online Resources===		===2026 SSAMM - Bioinformatics Tools and Online Resources===

			These are resources shared after discussions at the John Innes/Rudjer Bošković Summer School in Applied Molecular Microbiology in Dubrovnik in 2026

	====Strains====		====Strains====

	[http://streptomyces.org.uk Streptomyces.org] Links to resources including StrepDB and a free download of the Streptomyces manual.		[http://streptomyces.org.uk Streptomyces.org] Links to resources including StrepDB and a free download of the Streptomyces manual.

			[https://actinomycetes.bcco.cz/ Culture Collection of Actinomycetes] The CCA serves as a depository for cultures of environmental & clinical actinomycetes.

			[https://npdc.rc.ufl.edu/home Natural Products Discovery Centre Portal]. The world's largest natural products-focused collection of Actinobacteria and their curated draft genomes.

	[https://bacdive.dsmz.de/ BacDive (The Bacterial Diversity Metadatabase) ] The world’s largest database for standardized bacterial information. Look up your strain, its morphology, culture and growth condition, DNA sequence accessions, chemotaxonomic features etc.		[https://bacdive.dsmz.de/ BacDive (The Bacterial Diversity Metadatabase) ] The world’s largest database for standardized bacterial information. Look up your strain, its morphology, culture and growth condition, DNA sequence accessions, chemotaxonomic features etc.
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	====Biosynthetic gene cluster tools====		====Biosynthetic gene cluster tools====

	[https://antismash.secondarymetabolites.org antiSMASH] Very well-supported tool for BGC identification in bacterial~~, fungal and plant~~ genomes.		[https://antismash.secondarymetabolites.org antiSMASH] Very well-supported tool for BGC identification in bacterial genomes.

	[https://antismash-db.secondarymetabolites.org/ antiSMASH-db] Precomputed antiSMASH results for >200,000 BGC regions. Enables targeted searches and downloading of BGC regions.		[https://antismash-db.secondarymetabolites.org/ antiSMASH-db] Precomputed antiSMASH results for >200,000 BGC regions. Enables targeted searches and downloading of BGC regions.
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	[https://github.com/Merck/deepbgc DeepBGC] DeepBGC detects BGCs in bacterial and fungal genomes using deep learning. You can train the tool on your own data.		[https://github.com/Merck/deepbgc DeepBGC] DeepBGC detects BGCs in bacterial and fungal genomes using deep learning. You can train the tool on your own data.

			[https://fungismash.secondarymetabolites.org/#!/start FungiSMASH] Very well-supported tool for BGC identification in fungal genomes.

	[https://github.com/zellerlab/GECCO GECCO] BGC identification using a machine learning approach.		[https://github.com/zellerlab/GECCO GECCO] BGC identification using a machine learning approach.

	[https://github.com/chevrettelab/gator-gc GATOR-GC] Flexible tool for targeted genome mining of BGCs, genomic islands, resistance islands, and more. Allows for a customised approach to exploring and comparing gene clusters across any chosen genomic database.		[https://github.com/chevrettelab/gator-gc GATOR-GC] Flexible tool for targeted genome mining of BGCs, genomic islands, resistance islands, and more. Allows for a customised approach to exploring and comparing gene clusters across any chosen genomic database.

			[https://gutsmash.bioinformatics.nl/help.html GutSMASH] Extended Identification of Primary Metabolic Gene Clusters From the Human Gut Microbiota

	[https://biosyn.nih.go.jp/2ndfind/ 2ndFind] Tool to find specialised metabolite BGCs in bacterial or eukaryotic genome sequence. The tool finds secondary metabolism proteins using Pfam domains found in specialised metabolism proteins. Useful for rapid Pfam analysis of BGCs.		[https://biosyn.nih.go.jp/2ndfind/ 2ndFind] Tool to find specialised metabolite BGCs in bacterial or eukaryotic genome sequence. The tool finds secondary metabolism proteins using Pfam domains found in specialised metabolism proteins. Useful for rapid Pfam analysis of BGCs.
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	[https://github.com/Kalan-Lab/lsaBGC-Pan lsaBGC] Suite for pan-BGC-omics analysis		[https://github.com/Kalan-Lab/lsaBGC-Pan lsaBGC] Suite for pan-BGC-omics analysis

			[https://github.com/NPLinker/nplinker NPLinker2 GitHub] NPLinker 2 is a modular, customizable, and redesigned Python framework for paired omics analyses that prioritizes integrating and linking microbial genomics and metabolomics data

	[https://github.com/Kalan-Lab/zol Zol (& fai)] large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)		[https://github.com/Kalan-Lab/zol Zol (& fai)] large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)
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	[https://npdomainseeker.sdsc.edu/napdos2/ NaPDoS2] The Natural Product Domain Seeker rapidly detects and classifies ketosynthase and condensation domains from sequence data. It uses a phylogeny-based classification scheme to predict specific domain functions.		[https://npdomainseeker.sdsc.edu/napdos2/ NaPDoS2] The Natural Product Domain Seeker rapidly detects and classifies ketosynthase and condensation domains from sequence data. It uses a phylogeny-based classification scheme to predict specific domain functions.

			[https://paras.bioinformatics.nl/ PARAS] Predict the substrate specificity of adenylation domains in non-ribosomal peptide synthetases.

	====RiPP tools====		====RiPP tools====

PSET152

Matt Hutchings — Sat, 10 Oct 2026 09:28:37 GMT

References

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	{{DISPLAYTITLE: pSET152}}		{{DISPLAYTITLE: pSET152}}

			==Features==

	~~==Use==~~		• Backbone: Derived from a standard E. coli plasmid vector (pBR322/pUC lineage) containing an E. coli replication origin (ori) and an origin of transfer (oriT) derived from broad-host-range plasmid RK2 to allow conjugal transfer.

	~~==Features==~~		• Integrative Machinery: Incorporates the attachment site (attP) and the integrase gene (int) from the temperate actinophage φC31. Integrates into the φC31 att site on the Streptomyces genome.

			• Selection Marker: Carries the aac(3)IV gene, which confers resistance to apramycin in both E. coli and Streptomyces.

	==History==		==History==

			The pSET152 plasmid was constructed and published by Bierman et al. in 1992 as an E. coli–Streptomyces shuttle and integrative vector

	==Map==		==Map==
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	==References==		==References==

			M. Bierman, R. Logan, K. O'Brien, E.T. Seno, R. Nagaraja Rao, B.E. Schoner (1992). Plasmid cloning vectors for the conjugal transfer of DNA from Escherichia coli to Streptomyces spp. Gene 116:43-49.

			Abstract
			We have constructed cloning vectors for the conjugal transfer of DNA from Escherichia coli to Streptomyces spp. All vectors contain the 760-bp oriT fragment from the IncP plasmid, RK2. Transfer functions need to be supplied in trans by the E. coli donor strain. We have incorporated into these vectors selectable antibiotic-resistance markers (AmR, ThR, SpR) that function in Streptomyces spp. and other features that should allow for: (i) integration via homologous recombination between cloned DNA and the Streptomyces spp. chromosome, (ii) autonomous replication, or (iii) site-specific integration at the bacteriophage φC31 attachment site. Shuttle cosmids for constructing genomic libraries and bacteriophage P1 cloning vector capable of accepting approx. 100-kb fragments are also described. A simple mating procedure has been developed for the conjugal transfer of these vectors from E. coli to Streptomyces spp. that involves plating of the donor strain and either germinated spores or mycelial fragments of the recipient strain. We have shown that several of these vectors can be introduced into Streptomyces fradiae, a strain that is notoriously difficult to transform by PEG-mediated protoplast transformation.


			https://www.sciencedirect.com/science/article/abs/pii/0378111992906272

Methods

Matt Hutchings — Wed, 30 Sep 2026 10:32:52 GMT

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	This allows you to publish supplementary methods to support, and cite, in your publications. Email matt.hutchings@jic.ac.uk if you want to use this page or feel free to add them yourself if you have editing rights.

	Som N, Devine R, Chandra G, Martins C, Wilkinson B and Hutchings MI (2023). MtrA regulates the expression of developmental genes, including BldM and WhiI, in <em>Streptomyces venezuelae</em>. Manuscript in preparation. [[ MtrA methods are here]].