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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NCBI Assembly Archive Viewer Resource Report Resource Website 100+ mentions |
NCBI Assembly Archive Viewer (RRID:SCR_012917) | NCBI Assembly Archive Viewer | service resource, data set, data or information resource, data repository, storage service resource | Database providing information on structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data. The Archive links the raw sequence information found in the Trace Archive with assembly information found in publicly available sequence repositories (GenBank/EMBL/DDBJ). | sequence alignment, sequence chromatogram, assembly, virus |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is related to: GenBank is related to: Trace Archive is related to: DNA DataBank of Japan (DDBJ) is related to: European Nucleotide Archive (ENA) |
OMICS_00890, r3d100012688 | http://www.ncbi.nlm.nih.gov/assembly, https://doi.org/10.17616/R31NJMA8 | http://www.ncbi.nlm.nih.gov/Traces/assembly/assmbrowser.cgi | SCR_012917 | Assembly Archive Viewer, NCBI Assembly, Assembly | 2026-07-28 09:43:19 | 274 | ||||||
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Cystic Fibrosis Center - University of Washington Microbiology Core Resource Report Resource Website |
Cystic Fibrosis Center - University of Washington Microbiology Core (RRID:SCR_015403) | access service resource, service resource, resource, core facility | Core facility which provides tools, reagents, and training for microbiological researchers investigating cystic fibrosis. They specifically provide resources for research in anti-bacterial therapies, | anti-bacterial therapy, cystic fibrosis research, cystic fibrosis bacterial strain, cystic fibrosis bacteria provider |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Washington; Seattle; USA has parent organization: Cystic Fibrosis Center - University of Washington is organization facet of: Cystic Fibrosis Center - University of Washington |
Cystic Fibrosis | NIDDK P30DK089507 | Available to the research community | SCR_015403 | 2026-07-28 09:44:03 | 0 | ||||||||
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OrthoDB Resource Report Resource Website 500+ mentions |
OrthoDB (RRID:SCR_011980) | data or information resource, database | Database of orthologous protein coding genes across vertebrates, arthropods, fungi, basal metazoans, and bacteria. | Hierarchical catalog, ortholog, protein coding genes, mapping genomics to functional data, FASEB list |
is listed by: OMICtools has parent organization: University of Geneva; Geneva; Switzerland |
Swiss National Foundation | PMID:23180791 | Free, Freely available | OMICS_01692 | http://cegg.unige.ch/orthodb7 | SCR_011980 | OrthoDB: Database of Orthologous Groups, OrthoDB v7, OrthoDB - The Hierarchical Catalog of Orthologs, OrthoDB v10 | 2026-07-28 09:43:01 | 999 | |||||
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LPSN Database Resource Report Resource Website 100+ mentions |
LPSN Database (RRID:SCR_018151) | data or information resource, service resource, database | Database lists names of prokaryotes that have been validly published in International Journal of Systematic and Evolutionary Microbiology directly or by inclusion in Validation List, under Rules of International Code of Nomenclature of Bacteria. Has classification of prokaryotes and information on prokaryotic nomenclature and culture collections. | Collection, published Prokaryote name, International Journal of Systematic and Evolutionary Microbiology, prokaryotes classification, prokaryotes nomenclature, culture collection, data, FASEB list | DOI:10.1093/nar/gkt1111 | Free, Freely available | SCR_018151 | List of Prokaryotic names with Standing in Nomenclature Database | 2026-07-28 09:44:37 | 111 | |||||||||
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Carbohydrate Structure Database Resource Report Resource Website 1+ mentions |
Carbohydrate Structure Database (RRID:SCR_018684) | CSDB | data or information resource, database | Database contains manually curated natural carbohydrate structures, taxonomy, bibliography, NMR data. Bacterial and Plant and Fungal databases were merged to improve quality of content-dependent services, such as taxon clustering or NMR simulation. These separate databases will be supported in parallel until 2020. | Manually curated data, natural carbohydrate structure, carbohydrate taxonomy, carbohydrate bibliography, NMR data, bacterial carbohydrate data, fungal carbohydrate data, taxon clustering | is related to: Bacterial Carbohydrate Structure DataBase | Cooperative Threat Reduction Program of the US Department of Defense ; Russian Foundation for Basic Research ; Russian Science Foundation ; Russian Federation President program ; Deutsches Krebsforschungszentrum |
Free, Freely available | r3d100012862 | https://doi.org/10.17616/R3QZ33 | SCR_018684 | CSDB version 1 | 2026-07-28 09:44:48 | 7 | |||||
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xFITOM Resource Report Resource Website 1+ mentions |
xFITOM (RRID:SCR_014445) | software application, data analysis software, sequence analysis software, software resource, data processing software, standalone software | A fully customizable program that uses a graphical user interface to locate transcription factor-binding sites in genomic sequences. xFITOM scans DNA or RNA sequences for putative binding sites as defined by a collection of aligned known sites, a consensus sequence in IUPAC degenerate-base format, or a combination of the two. | transcription factor, binding site, information theory, customizable program, sequence analysis software |
uses: GenBank is related to: CollecTF |
PMID:21346861 | Available for download, Acknowledgement requested | http://www.mybiosoftware.com/fitom-1-0-detection-binding-sites-dna-rna-sequences.html | compbio.umbc.edu/Software/xFITOM/ http://research.umbc.edu/~erill/ | SCR_014445 | 2026-07-28 09:43:26 | 7 | |||||||
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OrthoVenn2 Resource Report Resource Website 100+ mentions |
OrthoVenn2 (RRID:SCR_022504) | software resource, data access protocol, web service | Web server for whole genome comparison and annotation of orthologous clusters across multiple species.Works on any operating system with modern browser and Javascript enabled. Used to identify orthologous gene clusters and supports user define species to upload customized protein sequences. Interactive graphic tool which provides Venn diagram view for comparing multiple species protein sequences. | whole genome comparison and annotation, orthologous clusters across multiple species, identify orthologous gene clusters, comparing multiple species protein sequences | National Natural Science Foundation of China | PMID:31053848 | Free, Freely available | SCR_022504 | 2026-07-28 09:45:39 | 255 | |||||||||
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BiGG Database Resource Report Resource Website 100+ mentions |
BiGG Database (RRID:SCR_005809) | BiGG | data or information resource, database | A knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest. | biochemical, genetics, genomics, genome, metabolic network, reconstruction, model, metabolic pathway, gene, protein, reaction, metabolite, metabolic reconstruction, compound, pathway, FASEB list |
uses: SBML is used by: BiGGR is listed by: 3DVC has parent organization: University of California at San Diego; California; USA |
NIH ; Ruth L. Kirschstein National Research Service Award - NIH Bioinformatics Training ; University of California at San Diego; California; USA ; Calit2 summer research scholarship ; NIGMS GM00806-06 |
PMID:20426874 | nlx_149299, r3d100011567 | https://doi.org/10.17616/R3MG9M | SCR_005809 | BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions, BiGG - a Biochemical Genetic and Genomic knowledgebase | 2026-07-28 09:41:21 | 124 | |||||
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DBETH - Database for Bacterial ExoToxins for Humans Resource Report Resource Website 1+ mentions |
DBETH - Database for Bacterial ExoToxins for Humans (RRID:SCR_005908) | DBETH | data or information resource, database | Database of Bacterial ExoToxins for Human is a database of sequences, structures, interaction networks and analytical results for 229 exotoxins, from 26 different human pathogenic bacterial genus. All toxins are classified into 24 different Toxin classes. The aim of DBETH is to provide a comprehensive database for human pathogenic bacterial exotoxins. DBETH also provides a platform to its users to identify potential exotoxin like sequences through Homology based as well as Non-homology based methods. In homology based approach the users can identify potential exotoxin like sequences either running BLASTp against the toxin sequences or by running HMMER against toxin domains identified by DBETH from human pathogenic bacterial exotoxins. In Non-homology based part DBETH uses a machine learning approach to identify potential exotoxins (Toxin Prediction by Support Vector Machine based approach). | sequence, structure, interaction network, human, pathogen, bacterial genus, toxin, bacteria, exotoxin, homology, homolog, structure, sequence, domain, prediction, mechanism, activity, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: CSIR - Indian Institute of Chemical Biology; Kolkata; India |
Council of Scientific and Industrial Research; New Delhi; India | PMID:22102573 | nlx_149481, biotools:dbeth | https://bio.tools/dbeth | SCR_005908 | Database for Bacterial ExoToxins for Humans | 2026-07-28 09:41:31 | 2 | |||||
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WebGeSTer DB Resource Report Resource Website 1+ mentions |
WebGeSTer DB (RRID:SCR_002165) | WebGeSTer DB | data or information resource, database | Database of intrinsic terminators of transcription that is comprized of >2,200,000 bacterial terminators identified from a total of 2036 chromosomes and 1508 plasmids. Information about structural parameters of individual terminators such as sequence, length of stem and loop, mismatches and gaps, U-trail, genomic coordinates and gene name and accession number is available in both tabular form and as a composite figure. Summary statistics for terminator profiles of whole genome can be also obtained. Raw data files for individual genomes can be downloaded (.zip files) for detailed investigations. Data is organized into different tiers such that users can fine-tune their search by entering name of the species, or taxon ID or genomes with a certain number of terminators. To visualize the occurrence of the terminators, an interactive map, with the resolution to single gene level, has been developed. | genome, terminator, transcription, plasmid, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20972211 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:webgester_db, OMICS_01862 | https://bio.tools/webgester_db | SCR_002165 | WebGesTer Database, Web Genome Scannner for Terminators Database, WebGeSTer DB - A Transcription Terminator Database | 2026-07-28 09:40:21 | 5 | |||||
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RegPrecise Resource Report Resource Website 50+ mentions |
RegPrecise (RRID:SCR_002149) | RegPrecise | data or information resource, database | Collection of manually curated inferences of regulons in prokaryotic genomes. Database for capturing, visualization and analysis of transcription factor regulons that were reconstructed by comparative genomic approach in wide variety of prokaryotic genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | regulon, genome, transcription factor, gene, operon, transcription factor binding site, taxonomy, rna, effector, pathway, ortholog, function, FASEB list |
is listed by: OMICtools has parent organization: Lawrence Berkeley National Laboratory |
Department of Energy ; NSF DBI-0850546 |
PMID:24175918 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01869 | SCR_002149 | 2026-07-28 09:40:21 | 80 | ||||||
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RefSeq Resource Report Resource Website 10000+ mentions |
RefSeq (RRID:SCR_003496) | data or information resource, database | Collection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases. | reference sequence, transcript, protein, dna, rna, plasmid, organelle, virus, genome, nucleic acid, ortholog, paralog, haplotype, nucleotide sequence, gene expression, blast, gold standard, bio.tools |
is listed by: OMICtools is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: BeetleBase is related to: EcoGene is related to: INSDC is related to: HFV Database is related to: RefSeqGene is related to: NCBI Protein Database is related to: RefSeqGene is related to: UniParc at the EBI is related to: NCBI Nucleotide is related to: UniParc is related to: ProRepeat is related to: NCBI Virus is related to: Codon and Codon-Pair Usage Tables is related to: RefSeq non-redundant proteins has parent organization: NCBI |
PMID:24316578 PMID:24259432 PMID:22121212 PMID:18927115 PMID:17130148 PMID:15608248 |
Free, Available for download, Freely available | SCR_016579, nif-0000-03397, OMICS_01659, biotools:refseq, r3d100011306 | ftp://ftp.ncbi.nlm.nih.gov/refseq, https://bio.tools/refseq, https://doi.org/10.17616/R3HP70 | SCR_003496 | RefSeq, , Reference Sequence Database, Reference Sequence, Reference Sequences, NCBI | 2026-07-28 09:40:43 | 18049 | ||||||
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NCBI Taxonomy Resource Report Resource Website 100+ mentions |
NCBI Taxonomy (RRID:SCR_003256) | NCBI Taxonomy | data or information resource, database | Database for a curated classification and nomenclature that contains the names of all organisms that are represented in the public sequence databases with at least one nucleotide or protein sequence. Data provided encompasses archaea, bacteria, eukaryota, viroids and viruses. The NCBI taxonomy database is not a primary source for taxonomic or phylogenetic information. Furthermore, the database does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based databases, and the advice of sequence submitters and outside taxonomy experts. Consequently, the NCBI taxonomy database is not a phylogenetic or taxonomic authority and should not be cited as such. | viroid, virus, nucleotide, protein, sequence, phylogeny, taxonomic, taxonomy, nomenclature, cladistics, classification, animal, genetic code, gold standard |
is used by: NIF Data Federation is used by: Vertebrate Taxonomy Ontology is listed by: re3data.org is related to: Taxonomy is related to: NEWT is related to: Phenoscape Knowledgebase is related to: EBIMed is related to: GOTaxExplorer is related to: Whatizit is related to: Integrated Manually Extracted Annotation has parent organization: NCBI is parent organization of: NCBITaxon |
PMID:18940862 PMID:18940867 |
Free, Freely available | nif-0000-03179, r3d100010776 | http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html, https://doi.org/10.17616/R3X039 | SCR_003256 | NCBI Taxonomy Browser, Taxonomy Browser, Entrez Taxonomy Browser, NCBI Taxonomy Database | 2026-07-28 09:40:39 | 273 | |||||
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PHI-base Resource Report Resource Website 100+ mentions |
PHI-base (RRID:SCR_003331) | PHI-base | data or information resource, database | Database that catalogs experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. It is an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, it also includes antifungal compounds and their target genes. Each entry is curated by domain experts and is supported by strong experimental evidence (gene disruption experiments, STM etc), as well as literature references in which the original experiments are described. Each gene is presented with its nucleotide and deduced amino acid sequence, as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, genes have been annotated using controlled vocabularies and links to external sources (Gene Ontology terms, EC Numbers, NCBI taxonomy, EMBL, PubMed and FRAC). | gene expression, pathogenic bacteria, virulence, infection, target site, gene, pathogen-host interaction, interaction, phenotype, pathogen, disease, host, anti-infective, nucleotide sequence, amino acid sequence, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian |
BBSRC BB/1000488/1 | PMID:17942425 PMID:17153929 PMID:16381911 |
Free, Freely available | nif-0000-03276, r3d100011301, biotools:phi-base | https://bio.tools/phi-base, https://doi.org/10.17616/R35D1V | http://www4.rothamsted.bbsrc.ac.uk/phibase/ | SCR_003331 | Pathogen Host Interaction base, Pathogen Host Interaction, Pathogen Host Interaction-Base | 2026-07-28 09:40:41 | 198 | |||
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cpnDB: A Chaperonin Database Resource Report Resource Website 1+ mentions |
cpnDB: A Chaperonin Database (RRID:SCR_002263) | cpnDB | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences. | chaperonin sequence, microbial ecology, phylogenetics, chaperonin, plastid, mitochondria, cytoplasm, sequence, blast, fasta, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Canadian Biotechnology Strategy ; National Research Council Genomics and Health Initiative |
PMID:15289485 | Free, Freely available | biotools:cpndb, OMICS_01511, nif-0000-02694 | https://bio.tools/cpndb | http://www.cpndb.ca/cpnDB/home.php | SCR_002263 | 2026-07-28 09:40:23 | 3 | ||||
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Pathosystems Resource Integration Center Resource Report Resource Website 1000+ mentions |
Pathosystems Resource Integration Center (RRID:SCR_004154) | PATRIC | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource, bioinformatics resource center | A Bioinformatics Resource Center bacterial bioinformatics database and analysis resource that provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. The PATRIC project includes three primary collaborators: the University of Chicago, the University of Manchester, and New City Media. The University of Chicago is providing genome annotations and a PATRIC end-user genome annotation service using their Rapid Annotation using Subsystem Technology (RAST) system. The National Centre for Text Mining (NaCTeM) at the University of Manchester is providing literature-based text mining capability and service. New City Media is providing assistance in website interface development. An FTP server and download tool are available. | genomics, genome, transcriptomics, protein-protein interaction, sequence typing, proteobacteria, brucella, rickettsia, coxiella, coronavirus, calicivirus, lyssavirus, virus, hepatitis a, hepatitis e, pathway, proteome, metabolic pathway, drug, vaccine, diagnostics, FASEB list |
is listed by: OMICtools has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA |
NIAID | PMID:24225323 PMID:17142235 |
Free, Public, Acknowledgement requested | r3d100010142, OMICS_01658, nlx_17476 | http://patricbrc.vbi.vt.edu/portal/portal/patric/Home, https://doi.org/10.17616/R3WS3X | http://patric.vbi.vt.edu/ | SCR_004154 | PathoSystems Resource Integration Center, PATRIC, Pathosystems Resource Integration Center | 2026-07-28 09:40:53 | 1083 | |||
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Genometa Resource Report Resource Website |
Genometa (RRID:SCR_001181) | Genometa | software resource | A Java based bioinformatics program which allows rapid analysis of metagenomic short read datasets. Millions of short reads can be accurately analysed within minutes and visualised in the browser component. A large database of diverse bacteria and archaea has been constructed as a reference sequence. The approach is based upon the established open source visualisation tool IGB and supported by the rapid alignment program bowtie. The Picard toolset for SAM files is also made use of. | metagenomic, classify, windows, linux, java, bio.tools, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Hannover Medical School; Lower Saxony; Germany |
PMID:22927906 | Free, Available for download, Freely available | biotools:genometa, OMICS_02175 | https://bio.tools/genometa | SCR_001181 | Genometa - Rapid analysis of metagenomic short reads | 2026-07-25 12:04:56 | 0 | |||||
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TSSer Resource Report Resource Website |
TSSer (RRID:SCR_006419) | TSSer | software resource | A computational pipeline to analyze differential RNA sequencing (dRNA-seq) data to determine transcription start sites genome-wide. | differential rna sequencing, transcription start site, rna-seq, genome, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Basel; Basel; Switzerland |
PMID:24371151 | GNU General Public License | biotools:tsser, OMICS_02191 | https://bio.tools/tsser | SCR_006419 | TSSer: a computational pipeline to identify transcription start sites in bacterial genomes | 2026-07-25 12:06:23 | 0 | |||||
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LMAT Resource Report Resource Website 10+ mentions |
LMAT (RRID:SCR_004646) | LMAT | software resource | Open-source software tool to assign taxonomic labels to as many reads as possible in very large metagenomic datasets and report the taxonomic profile of the input sample. The quick "single pass" analysis of every read allows read binning to support additional more computationally expensive analysis such as metagenomic assembly or sensitive database searches on targeted subsets of reads. | c++, metagenomic, metagenomic classification, genome, virus, taxonomy, database, reference genome |
is listed by: OMICtools has parent organization: Lawrence Livermore National Laboratory has parent organization: SourceForge |
PMID:23828782 | Open unspecified license | OMICS_02285 | SCR_004646 | Livermore Metagenomics Analysis Toolkit | 2026-07-25 12:05:52 | 15 | ||||||
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PathSeq Resource Report Resource Website 50+ mentions |
PathSeq (RRID:SCR_005203) | PathSeq | software resource | A computational tool for the identification and analysis of microbial sequences in high-throughput human sequencing data that is designed to work with large numbers of sequencing reads in a scalable manner. This process is composed of a subtractive phase in which input reads are subtracted by alignment to human reference sequences, and an analytic phase in which the remaining reads are aligned to microbial reference sequences (viral, fungal, bacterial, archaeal) and de novo assembled. PathSeq is currently available in a cloud computing environment via Amazon Web Services The typical approach one would take to pathogen discovery with PathSeq: RNA or DNA is extracted from the tissue of interest and sequencing libraries are constructed to be run on the next-generation DNA sequencing platform of choice. The resulting sequence data is run through the PathSeq pipeline in a cloud computing environment. PathSeq reports potential microbes in the sequence data as well as the complete set of reads that could not be identified as human or microbial sequences. | virus, microbe, pathogen, dna, rna, next-generation sequencing |
is listed by: OMICtools is related to: Amazon Web Services has parent organization: Broad Institute |
PMID:21552235 | Acknowledgement requested, Account required, (for Amazon Web Services and you will need to pay for the AWS resource time) | OMICS_00221 | SCR_005203 | PathSeq: Pathogen Discovery | 2026-07-25 12:06:00 | 62 |
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