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

← Older revision		Revision as of 14:45, 19 October 2026
(12 intermediate revisions by the same user not shown)
Line 1:		Line 1:
	===~~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.
Line 49:		Line 55:
	====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.
Line 74:		Line 80:

	[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.
Line 84:		Line 94:

	[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.)
Line 94:		Line 106:

	[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====

ActinoBase - Recent changes [en-gb]

User:AndyT

Bioinformatics