Useful resources can be found here - Revision history

Matt Hutchings at 11:06, 14 November 2024

2024-11-14T11:06:19Z

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	[https://www.blender.org Blender 3D] Animation tool that can be used to create scientific animations. There are hundreds of tutorials for Blender to get started, but these are a great starting point for a science-focussed approach:		[https://www.blender.org Blender 3D] Animation tool that can be used to create scientific animations. There are hundreds of tutorials for Blender to get started, but these are a great starting point for a science-focussed approach:

	https://www.youtube.com/watch?v=CfkjBoOaw0g		https://www.youtube.com/watch?v=CfkjBoOaw0g<br>
	https://www.youtube.com/watch?v=zXJKYvuCPYY		https://www.youtube.com/watch?v=zXJKYvuCPYY

Matt Hutchings at 11:05, 14 November 2024

2024-11-14T11:05:37Z

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	[https://www.kbase.us/ KBase] KBase integrates a variety of data and analysis tools to perform sophisticated systems biology analyses.		[https://www.kbase.us/ KBase] KBase integrates a variety of data and analysis tools to perform sophisticated systems biology analyses.
	~~Snakemake~~ https://snakemake.readthedocs.io/en/stable/ Make pipelines out of multiple tools.
			[https://snakemake.readthedocs.io/en/stable/ Snakemake] Make pipelines out of multiple tools.

			====Other====

			[https://github.com/Arkadiy-Garber/FeGenie FeGenie] HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes.

			[https://radicalsam.org/ RadicalSAM.org] Online database of radical SAM enzymes categorised into sequence similarity networks. Integrates further information, including genomic neighbourhoods and associated conserved domains.

			[https://www.blender.org Blender 3D] Animation tool that can be used to create scientific animations. There are hundreds of tutorials for Blender to get started, but these are a great starting point for a science-focussed approach:

			https://www.youtube.com/watch?v=CfkjBoOaw0g
			https://www.youtube.com/watch?v=zXJKYvuCPYY

Matt Hutchings at 11:04, 14 November 2024

2024-11-14T11:04:04Z

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	[https://merenlab.org/software/ Anvi'o] An advanced analysis and visualization platform for ‘omics data.		[https://merenlab.org/software/ Anvi'o] An advanced analysis and visualization platform for ‘omics data.

			====General bioinformatic sequence tools/resources====

			[https://usegalaxy.org/ Galaxy] User-friendly server with a lot of bioinformatic tools.

			[https://bioinf.shenwei.me/seqkit/ SeqKit] Various sequence file manipulation tools in Terminal.

			[https://www.ncbi.nlm.nih.gov/books/NBK179288/ Entrez Direct (EDirect)] Provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a command line: useful to automatically retrieve information from genomes/metagenomes.

			[https://www.phylo.org/ CIPRES] Portal for online phylogenetic tools that runs jobs on NSF resources in the USA.

			[https://www.kbase.us/ KBase] KBase integrates a variety of data and analysis tools to perform sophisticated systems biology analyses.
			Snakemake https://snakemake.readthedocs.io/en/stable/ Make pipelines out of multiple tools.

Matt Hutchings at 11:02, 14 November 2024

2024-11-14T11:02:28Z

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	[https://www.npatlas.org/discover/snapms/ SNAP-MS] Tool integrated into the NP Atlas for the prediction of natural product compound classes using mass spectrometry data.		[https://www.npatlas.org/discover/snapms/ SNAP-MS] Tool integrated into the NP Atlas for the prediction of natural product compound classes using mass spectrometry data.

			====Data visualisation====

			[https://www.jalview.org/ Jalview] Java-based GUI tool for sequence analysis (alignments etc) and visualisation.

			[https://www.cgl.ucsf.edu/chimerax/ ChimeraX] Open-access protein structure analysis and visualisation software.

			[https://cmdcolin.github.io/awesome-genome-visualization/?latest=true Awesome genome visualisation] Resource listing many different genome visualisation tools.

			[https://merenlab.org/software/ Anvi'o] An advanced analysis and visualization platform for ‘omics data.

Matt Hutchings at 11:00, 14 November 2024

2024-11-14T11:00:56Z

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	[https://npmrd-project.org/ Natural Product Magnetic Resonance Database Project (NP-MRD)] Online database for community deposition of NMR data relating to natural products.		[https://npmrd-project.org/ Natural Product Magnetic Resonance Database Project (NP-MRD)] Online database for community deposition of NMR data relating to natural products.

			====Metabolomics====

			[https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp GNPS] analyse and compare mass spectrometry (MS/MS) data - within your dataset, with standards and with community datasets [https://massive.ucsd.edu/ProteoSAFe/ (deposited in MASSive database)] there are many integrated tools (some of which are listed below), ReDu lets you reanalyse your data, MS2LDA (below), feature based molecular network (allows you to characterise your data into molecular types), DEREPLICATOR+ (in silico annotation) etc.

			[https://v6.docs.sirius-ms.io/ SIRIUS] Tool for the structure prediction/elucidation of novel molecules using MS data.

			[https://www.metaboanalyst.ca/ MetaboAnalyst] Online platform for the analysis and interpretation of metabolomics data and integration with other omics data.

			[https://systemsomicslab.github.io/compms/msdial/main.html MS-Dial] Open source metabolomics analysis software.

			[http://mzmine.github.io/ mzMine3] Open source metabolomics analysis software that supports multimodal data analysis for various instrumental setups, including LC and GC–MS, and ion mobility.

			[https://ccms-ucsd.github.io/GNPSDocumentation/ms2lda/ MSL2DA] decomposes molecular fragmentation data derived from large metabolomics experiments into annotated Mass2Motifs (substructures).

			[https://massql.gnps2.org/ MassQL] Formulates queries to find these patterns in raw mass spectrometry (set e.g. retention time, scan number etc) data.

			[https://pypi.org/project/matchms/0.14.0/ MATCHMS] Imports, processes, cleans, and compare mass spectrometry data (MS/MS).

			[https://github.com/madeleineernst/pyMolNetEnhancer MOLNET ENHANCER] Combines the outputs from molecular networking, MS2LDA, in silico annotation tools (such as Network Annotation Propagation or DEREPLICATOR), and automated chemical classification to provide a more comprehensive chemical overview of metabolomics data.

			[https://github.com/danielatrivella/NP3_MS_Workflow NP3 MS Workflow] Open-source tool for analysing untargeted metabolomic data from LC–MS/MS, designed to help identify bioactive natural products from complex mixtures. It offers customizable steps and clear statistical outputs, with features like MS2 spectrum processing, [M + H]+ ion deconvolution, and structural annotation.

			[https://www.npatlas.org/discover/snapms/ SNAP-MS] Tool integrated into the NP Atlas for the prediction of natural product compound classes using mass spectrometry data.

Matt Hutchings at 10:57, 14 November 2024

2024-11-14T10:57:46Z

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	[https://ggdc.dsmz.de/ GGDC (Genome-to-Genome Distance Calculator)] Calculate phylogenetic trees and pairwise gene sequence similarities. Also includes a tool for Single-Gene Trees.		[https://ggdc.dsmz.de/ GGDC (Genome-to-Genome Distance Calculator)] Calculate phylogenetic trees and pairwise gene sequence similarities. Also includes a tool for Single-Gene Trees.

			====Natural product databases====

			[https://www.npatlas.org/ The Natural Product Atlas] Searchable community-led directory of NPs.

			[https://lotus.naturalproducts.net/ LOTUS] Community-curated open source project for the storage, search and analysis of natural products data.

			[https://dnp.chemnetbase.com/faces/chemical/ChemicalSearch.xhtml Dictionary of Natural Products] Searchable directory of NPs (full version requires payment but some functions available for free).

			[https://npmrd-project.org/ Natural Product Magnetic Resonance Database Project (NP-MRD)] Online database for community deposition of NMR data relating to natural products.

Matt Hutchings at 10:56, 14 November 2024

2024-11-14T10:56:18Z

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	[https://card.mcmaster.ca The Comprehensive Antibiotic Database (CARD)] A rigorously curated collection of characterised resistance determinants and associated antibiotics. It also incorporates a tool called the Resistance Gene Identifier, which can predict resistance genes present in an input genome based on homology and SNP models.		[https://card.mcmaster.ca The Comprehensive Antibiotic Database (CARD)] A rigorously curated collection of characterised resistance determinants and associated antibiotics. It also incorporates a tool called the Resistance Gene Identifier, which can predict resistance genes present in an input genome based on homology and SNP models.

			====Systematics/Phylogeny====

			[https://automlst.ziemertlab.com/ Automated Multi-Locus Species Tree (autoMLST)] Online tool for automatic generation of species phylogeny with reference organisms.

			[https://bitbucket.org/ziemertlab/automlst/src/master/ autoMLST command line] Command line version for local installations of autoMLST.

			[https://github.com/biobakery/phylophlan PhyloPhlAn] An integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes.

			[https://itol.embl.de/ iTOL] Editing and visualization of phylogenetic/phylogenomic trees.

			[https://tygs.dsmz.de/ Type (Strain) Genome Server] Assesses whether a submitted strain is a novel species based on whole genome analysis. It also creates a whole genome phylogeny with closely related strains.

			[https://gtdb.ecogenomic.org/ Genome Taxonomy Database (GTDB)] Species classification

			[https://antonellilab.github.io/raxmlGUI/ raxmlGUI 2.0] GUI interface for using RaxML for phylogenetic inference using maximum likelihood (personal experience is that it can struggle with large trees on a personal computer - simply a challenge of processing power)

			[https://ggdc.dsmz.de/ GGDC (Genome-to-Genome Distance Calculator)] Calculate phylogenetic trees and pairwise gene sequence similarities. Also includes a tool for Single-Gene Trees.

Matt Hutchings at 10:54, 14 November 2024

2024-11-14T10:54:05Z

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	[https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi NCBI Conserved Domain Search] Search for conserved domains in proteins. Can analyse batches of protein sequences.		[https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi NCBI Conserved Domain Search] Search for conserved domains in proteins. Can analyse batches of protein sequences.

			====Antibiotic resistance====

			[https://arts.ziemertlab.com ARTS] A tool for looking for potential resistance genes/duplicated housekeeping genes in BGCs, as well as potentially unique metabolism.

			[https://card.mcmaster.ca The Comprehensive Antibiotic Database (CARD)] A rigorously curated collection of characterised resistance determinants and associated antibiotics. It also incorporates a tool called the Resistance Gene Identifier, which can predict resistance genes present in an input genome based on homology and SNP models.

Matt Hutchings at 10:53, 14 November 2024

2024-11-14T10:53:04Z

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	[https://github.com/Alexamk/decRiPPter decRiPPter] Data-driven Exploratory Class-independent RiPP TrackER. Machine learning tool for the detection of RiPP precursor peptides and associated BGCs.		[https://github.com/Alexamk/decRiPPter decRiPPter] Data-driven Exploratory Class-independent RiPP TrackER. Machine learning tool for the detection of RiPP precursor peptides and associated BGCs.

			====Protein structure and sequence analysis====

			https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb ColabFold] User-friendly protein structure and complex prediction using AlphaFold2 and Alphafold2-multimer.

			[https://alphafoldserver.com/ AlphaFold3] Online server for acquiring AlphaFold3 structure and complex predictions.

			[https://search.foldseek.com/search FoldSeek] Online server that enables fast protein structure alignments against large protein structure databases.

			[https://efi.igb.illinois.edu/efi-est/ EFI-EST] Generates protein similarity sequence networks (SSNs).

			[https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi NCBI Conserved Domain Search] Search for conserved domains in proteins. Can analyse batches of protein sequences.

Matt Hutchings at 10:51, 14 November 2024

2024-11-14T10:51:31Z

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	[http://nrps.igs.umaryland.edu/ NRPS-PKS] NRPS-PKS domain identification and specificity code prediction.		[http://nrps.igs.umaryland.edu/ NRPS-PKS] NRPS-PKS domain identification and specificity code prediction.

			====RiPP tools====

			[https://webtool.ripp.rodeo/ RODEO] and [https://www.ripp.rodeo/advanced.html RODEO advanced] Online tool for RiPP identification, and can also be used to retrieve and analyse gene neighbourhoods.

			[http://bagel5.molgenrug.nl/ BAGEL] Online tool for the detection of bacteriocins and RiPP BGCs in bacterial (meta-)genomes.

			[http://www.nii.ac.in/rippminer2.html RiPPMiner] Prediction of RiPP BGCs, RiPP families and RiPP product structures.

			[https://github.com/mohimanilab/seq2ripp seq2ripp] Identifies RiPPs from paired genomic and mass spectrometry data.

			[https://hyporippatlas.npanalysis.org/ HypoRiPPAtlas] Database of hypothetical RiPPs from RefSeq microbial genomes and plant transcriptomes. Data acquired using seq2ripp.

			[https://github.com/Alexamk/decRiPPter decRiPPter] Data-driven Exploratory Class-independent RiPP TrackER. Machine learning tool for the detection of RiPP precursor peptides and associated BGCs.