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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 | data repository, service resource, storage service resource, data or information resource, data set | 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 | 2026-02-12 09:45:45 | 274 | ||||||
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Genomes Online Database Resource Report Resource Website 100+ mentions |
Genomes Online Database (RRID:SCR_002817) | GOLD | data repository, service resource, storage service resource, database, data or information resource | Database of information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. It also provides information related to organism properties such as phenotype, ecotype and disease. Both complete and ongoing projects, along with their associated metadata, can be accessed. Users can also register, annotate and publish genome and metagenome data. | genome, genetics, metagenome, biosample, phenotype, ecotype, disease, sequencing, FASEB list |
is listed by: re3data.org has parent organization: DOE Joint Genome Institute |
PMID:22135293 PMID:19914934 PMID:17981842 PMID:16381880 PMID:11125068 PMID:10498782 |
Free, Freely available, Available for download | r3d100010808, nif-0000-02918 | https://doi.org/10.17616/R39310 | SCR_002817 | Genomes On Line Database (GOLD), GOLD:Genomes Online Database | 2026-02-12 09:43:27 | 159 | |||||
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National Center for Marine Algae and Microbiota Resource Report Resource Website 50+ mentions |
National Center for Marine Algae and Microbiota (RRID:SCR_002120) | NCMA | organism supplier, material resource, biomaterial supply resource | National marine phytoplankton collection, maintaining over 2700 strains from around the world, most are marine phytoplankton but they also have benthic, macrophytic, freshwater and heterotrophic organisms - now incorporating bacteria and viruses. Strain records have (when available): * collection and isolation information * culturing medium recipes and growth conditions * photographs * GenBank accession link * collection site map * link to the taxonomic database Micro*scope The deposition of new strains are welcome if the strains are a valuable addition to the collection. Examples include strains that are referred to in publications, contain interesting molecular, biochemical or physiological properties, are the basis for taxonomic descriptions, are important for aquaculture, or are from an unusual geographical location or ecological habitat. The NCMA offers a course in phytoplankton culturing techniques and facilities for visiting scientists are available at the new laboratories in East Boothbay, Maine. Services include: Mass Culturing DNA and RNA, Purification, Private Holdings, Culture Techniques Course, Visiting Scientists, Single Cell Genomics, Flow Cytometry, Corporate Alliances and Technology Transfer. | marine phytoplankton, marine, phytoplankton, virus, benthic, macrophytic, freshwater, heterotrophic, microbiota, seawater, FASEB list |
is listed by: One Mind Biospecimen Bank Listing is listed by: CINERGI |
NSF | Restricted | nlx_154729 | SCR_002120 | Provasoli-Guillard National Center for Culture of Marine Phytoplankton, Provasoli-Guillard National Center for Marine Algae and Microbiota, CCMP | 2026-02-12 09:43:18 | 53 | ||||||
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Protein Lounge Resource Report Resource Website 10+ mentions |
Protein Lounge (RRID:SCR_002117) | ProteinLounge | analysis service resource, training material, service resource, production service resource, database, narrative resource, data analysis service, data or information resource | Complete siRNA target database, complete Peptide-Antigen target database and a Kinase-Phosphatase database. They have also developed the largest database of illustrated signal transduction pathways, which are interconnected to their extensive protein database and online gene / protein analysis tools. The interactive web-based databases and software help life-scientists understand the complexity of systems biology. Systems biology efforts focus on understanding cellular networks, protein interactions involved in cell signaling, mechanisms of cell survival and apoptosis leading to development or identification of drug candidates against a variety of diseases. In the post-genomic era, one of the major concerns for life-science researchers is the organization of gene / protein data. Protein Lounge has met this concern by organizing all necessary data about genes / proteins into one portal. | gene, antigen, bioinformatics, kinase, life science, peptide, phosphatase, signal transduction pathway, sirna, systems biology, protein, biology, cellular network, protein interaction, cell signaling, cell survival, apoptosis, peptide-antigen, kinase-phosphatase, image, pathway | Restricted | nif-0000-20903 | SCR_002117 | Protein Lounge - Redefining Biology | 2026-02-12 09:43:18 | 29 | ||||||||
|
NCBI Genome Resource Report Resource Website 500+ mentions |
NCBI Genome (RRID:SCR_002474) | Genome | data repository, service resource, storage service resource, database, data or information resource | Database that organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations in six major organism groups: Archaea, Bacteria, Eukaryotes, Viruses, Viroids, and Plasmids. Genomes of over 1,200 organisms can be found in this database, representing both completely sequenced organisms and those for which sequencing is in progress. Users can browse by organism, and view genome maps and protein clusters. Links to other prokaryotic and archaeal genome projects, as well as BLAST tools and access to the rest of the NCBI online resources are available. | chromosome, organelle, plasmid, viroid, virus, genome, sequence, map, assembly, annotation, gene mapping, dna, blast, protein cluster, gold standard |
is listed by: re3data.org is related to: MapViewer is related to: UniProt Proteomes is related to: CaspBase has parent organization: NCBI |
Free, Freely avaialble | nif-0000-02802, r3d100010785 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome https://doi.org/10.17616/R3R89S |
SCR_002474 | Entrez Genomes, Entrez Genome, NCBI, Genome, Genome Database, Genome: Information by genome sequence | 2026-02-12 09:43:22 | 577 | ||||||
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BSRD Resource Report Resource Website 10+ mentions |
BSRD (RRID:SCR_004249) | BSRD | data repository, service resource, storage service resource, database, data or information resource | A repository for bacterial small regulatory RNA. They welcome you to submit new experimental validated sRNA targets. | srna target, srna, small regulatory non-coding rna, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:23203879 | Acknowledgement requested, The community can contribute to this resource | biotools:bsrd, OMICS_01533 | https://bio.tools/bsrd | SCR_004249 | BSRD - Bacterial Small Regulatory RNA Database, Bacterial Small Regulatory RNA Database | 2026-02-12 09:43:47 | 29 | |||||
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cpnDB: A Chaperonin Database Resource Report Resource Website 1+ mentions |
cpnDB: A Chaperonin Database (RRID:SCR_002263) | cpnDB | analysis service resource, service resource, production service resource, database, data analysis service, data or information 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 | 2026-02-12 09:43:20 | 3 | ||||
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Pathosystems Resource Integration Center Resource Report Resource Website 1000+ mentions |
Pathosystems Resource Integration Center (RRID:SCR_004154) | PATRIC | analysis service resource, service resource, production service resource, bioinformatics resource center, database, data analysis service, data or information resource | 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 | 2026-02-12 09:43:45 | 1083 | |||
|
xFITOM Resource Report Resource Website 1+ mentions |
xFITOM (RRID:SCR_014445) | sequence analysis software, standalone software, software resource, software application, data analysis software, data processing 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 | 2026-02-12 09:46:17 | 7 | |||||||
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AmphoraNet Resource Report Resource Website 10+ mentions |
AmphoraNet (RRID:SCR_005009) | AmphoraNet | service resource, analysis service resource, production service resource, data analysis service | 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 | 2026-02-12 09:44:03 | 16 | ||||||
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CW-PRED Resource Report Resource Website 10+ mentions |
CW-PRED (RRID:SCR_006188) | CW-PRED | service resource, analysis service resource, production service resource, data analysis service | 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 | 2026-02-12 09:44:19 | 16 | |||||||
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PRED-TMBB Resource Report Resource Website 50+ mentions |
PRED-TMBB (RRID:SCR_006190) | PRED-TMBB | service resource, analysis service resource, production service resource, data analysis service | 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 | 2026-02-12 09:44:18 | 54 | ||||
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OrthoVenn2 Resource Report Resource Website 100+ mentions |
OrthoVenn2 (RRID:SCR_022504) | software resource, web service, data access protocol | 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 | 2026-02-12 09:47:38 | 255 | |||||||||
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Vector Database Resource Report Resource Website 1+ mentions |
Vector Database (RRID:SCR_005907) | Vector Database | material resource, biomaterial supply resource | Vector database is a digital collection of vector backbones assembled from publications and commercially available sources. This is a free resource for the scientific community that is compiled by Addgene. Only the plasmids deposited at Addgene are available for purchase through this website. | vector, vector backbone, plasmid, mammalian expression, bacterial expression, retroviral, lentiviral, worm expression, insect expression, yeast expression, rnai, luciferase, mouse targeting, mammalian, bacterial, yeast, worm, insect, mouse, adenoviral, rnai, cre/lox, marker, neomycin, puromycin, hygromycin, zeocin, blasticidin, gentamicin, bacterial resistance, ampicillin, kanamycin, chloramphenicol, hygromycin, bleocin, zeocin |
is listed by: One Mind Biospecimen Bank Listing is related to: ATCC has parent organization: Addgene |
Free | nlx_149479 | SCR_005907 | Addgene Vector Database | 2026-02-12 09:44:20 | 6 | |||||||
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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) | service resource, access service resource, core facility, resource | 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 | 2026-02-12 09:46:31 | 0 | ||||||||
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LPSN Database Resource Report Resource Website 100+ mentions |
LPSN Database (RRID:SCR_018151) | data or information resource, database, service resource | 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 | 2026-02-12 09:47:24 | 111 | |||||||||
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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 | 2026-02-07 02:06:51 | 15 | ||||||
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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 | 2026-02-07 02:07:06 | 0 | |||||
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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 | 2026-02-07 02:05:32 | 0 | |||||
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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 | 2026-02-07 02:06:41 | 60 |
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