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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
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 2026-08-03 09:32:56 124
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 2026-08-03 09:32:57 2
CW-PRED
 
Resource Report
Resource Website
10+ mentions
CW-PRED (RRID:SCR_006188) CW-PRED data analysis service, service resource, analysis service resource, production service resource A web tool for the prediction of Cell Wall-Anchored Proteins in Gram+ Bacteria. Gram-positive bacteria have surface proteins that are often implicated in virulence. A group of extracellular proteins attached to the cell wall contains an LPXTG-like motif that is target for cleavage and covalent coupling to peptidoglycan by sortase enzymes. A new Hidden Markov Model (HMM), an extension to the HMM model from Litou et al., http://www.ncbi.nlm.nih.gov/pubmed/18464329, was developed for predicting the LPXTG and LPXTG-like cell-wall proteins of Gram-positive bacteria. An analysis of 177 completely sequenced genomes has been performed as well. We identified in total 1456 cell-wall proteins, from which 1283 have the LPXTG motif, 39 the NPXTG motif, 53 have the LPXTA and 81 the LAXTG motif. hidden markov model, gram-positive bacteria, protein, classification, cell-wall protein has parent organization: University of Athens Biophysics and Bioinformatics Laboratory Free for academic use, Acknowledgement requested nlx_151733 SCR_006188 CW-PRED: A HMM-based method for the classification of cell wall-anchored proteins of Gram-positive bacteria 2026-08-03 09:32:55 16
PRED-TMBB
 
Resource Report
Resource Website
50+ mentions
PRED-TMBB (RRID:SCR_006190) PRED-TMBB data analysis service, service resource, analysis service resource, production service resource A web tool, based on a Hidden Markov Model, capable of predicting the transmembrane beta-strands of the gram-negative bacteria outer membrane proteins, and of discriminating such proteins from water-soluble ones when screening large datasets. The model is trained in a discriminative manner, aiming at maximizing the probability of the correct prediction rather than the likelihood of the sequences. The training is performed on a non-redundant database consisting of 16 outer membrane proteins (OMP''s) with their structures known at atomic resolution. We show that we can achieve predictions at least as good comparing with other existing methods, using as input only the amino-acid sequence, without the need of evolutionary information included in multiple alignments. The method is also powerful when used for discrimination purposes, as it can discriminate with a high accuracy the outer membrane proteins from water soluble in large datasets, making it a quite reliable solution for screening entire genomes. This web-server can help you run a discriminating process on any amino-acid sequence and thereafter localize the transmembrane strands and find the topology of the loops. protein, hidden markov model, prediction, membrane protein, beta-barrel outer membrane protein, gram-negative bacteria, topology, outer membrane protein, beta-barrel protein, probability, transmembrane strand, bio.tools, FASEB list is listed by: bio.tools
is listed by: Debian
has parent organization: University of Athens Biophysics and Bioinformatics Laboratory
Greek Ministry of National Education and Religious Affairs PMID:15215419
PMID:15070403
Acknowledgement requested biotools:pred-tmbb, nlx_151734 https://bio.tools/pred-tmbb SCR_006190 PRED-TMBB: A Hidden Markov Model method capable of predicting and discriminating beta-barrel outer membrane proteins 2026-08-03 09:33:01 54
GBrowse
 
Resource Report
Resource Website
10+ mentions
GBrowse (RRID:SCR_006829) GBrowse data or information resource, database A database and interactive web site for manipulating and displaying annotations on genomes. Features include: detailed views of the genome; use of a variety of premade or personally made glyphs ; customizable order and appearance of tracks by administrators and end-users; search by annotation ID, name, or comment; support of third party annotation using GFF formats; DNA and GFF dumps; connectivity to different databases, including BioSQL and Chado; and a customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers, etc.). GBrowse is distributed as source code for Macintosh OS X, UNIX and Linux platforms, and as pre-packaged binaries for Windows machines. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. The wiki portion accepts data submissions. genome, annotation, database, perl, virus, dna, protein, reference sequence, chromosome, visualization, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is related to: WormBase
is related to: FlyBase
is related to: International HapMap Project
has parent organization: Generic Model Organism Database Project
has parent organization: Indiana University; Indiana; USA
Howard Hughes Medical Institute ;
NHGRI HG00739;
NHGRI P41HG02223
PMID:19957275
PMID:18428797
PMID:12368253
PMID:21400697
PMID:20194461
PMID:19357095
DOI:10.1002/0471250953.bi0909s28
The community can contribute to this resource, Requires Perl 5.8.6 or higher and the Apache web server OMICS_00910, biotools:gbrowse, nif-0000-30597 http://gmod.org/wiki/GBrowse, https://bio.tools/gbrowse, https://sources.debian.org/src/gbrowse/ SCR_006829 Generic Genome Browser 2026-08-03 09:33:11 43
5S Ribosomal RNA Database
 
Resource Report
Resource Website
1+ mentions
5S Ribosomal RNA Database (RRID:SCR_007545) 5S Ribosomal RNA Database data or information resource, database A database on nucleotide sequences of 5S rRNAs and their genes. The database contains 1985 primary structures of 5S rRNA and 5S rDNA, and was last updated in 2002, according to the website. They include 60 archaebacterial, 470 eubacterial, 63 plastid, nine mitochondrial and 1383 eukaryotic sequences. The nucleotide sequences of the 5S rRNAs or 5S rDNAs are divided according to the taxonomic position of the source organisms. The sequences for particular organisms can be retrieved as single files using a taxonomic browser or in multiple sequence structural alignments. The multiple sequence alignments of 5S ribosomal RNAs can be downloaded in TAB-delimited and FASTA formats. eubacteria, eukaryote, archaebacteria, mitochondrion, model rna molecule, nucleotide sequence database, ribosome, plastid, ribosomal rna, sequence alignment, rna-protein interaction, rna, rna structure, 5s rrna, gene, 5s rdna, mitochondria, sequence, alignment has parent organization: Polish Academy of Sciences Warsaw; Warsaw; Poland Deutsche Agentur fur Raumfahrtangelegenheiten GmbH ;
Fonds der Chemischen Industrie e.V. ;
Polish State Committee for Scientific Research ;
DFG
PMID:10592212 nif-0000-02526 http://rose.man/poznan. pl/5SData/index.html SCR_007545 2026-08-03 09:33:33 6
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 2026-08-03 09:32:25 18049
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 2026-08-03 09:32:02 273
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 2026-08-03 09:32:04 198
AmphoraNet
 
Resource Report
Resource Website
10+ mentions
AmphoraNet (RRID:SCR_005009) AmphoraNet data analysis service, service resource, analysis service resource, production service resource Webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data. It is capable of assigning a probability-weighted taxonomic group for each phylogenetic marker gene found in the input metagenomic sample. dna sequence, amino acid sequence, dna, sequence, amino acid, phylogenetic, reliability score, nucleotide, protein, nucleotide sequence, protein sequence, phylogenetic analysis, metagenomic, metagenomics, phylotyping, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Eotvos Lorand University; Budapest; Hungary
PMID:24144838 Acknowledgement requested, Free, Public biotools:amphoranet, OMICS_01450 https://bio.tools/amphoranet SCR_005009 2026-08-03 09:32:46 16
Cystic Fibrosis Center - University of Washington Microbiology Core
 
Resource Report
Resource Website
Cystic Fibrosis Center - University of Washington Microbiology Core (RRID:SCR_015403) resource, service resource, access service 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 2026-08-03 09:36:14 0
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 2026-08-03 09:31:35 5
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 2026-08-03 09:31:40 80
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 2026-08-03 09:34:54 999
LPSN Database
 
Resource Report
Resource Website
100+ mentions
LPSN Database (RRID:SCR_018151) service resource, data or information 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 2026-08-03 09:37:12 111
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 2026-08-03 09:37:18 7
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 2026-08-01 12:02:43 15
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 2026-08-01 12:02:57 62
READSCAN
 
Resource Report
Resource Website
1+ mentions
READSCAN (RRID:SCR_005204) READSCAN software resource A highly scalable parallel software program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. pathgen, genome, sequence, high-throughput sequence, align, read, host, microbe, virus, taxon, simulation, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia
PMID:23193222 OMICS_00222, biotools:readscan https://bio.tools/readscan SCR_005204 2026-08-01 12:02:47 5
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 2026-08-01 12:01:34 0

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