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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Ontogenesis Resource Report Resource Website 1+ mentions |
Ontogenesis (RRID:SCR_005380) | Ontogenesis | data or information resource, narrative resource, blog, training material | Knowledge Blog for descriptive, tutorial and explanatory material about building, using and maintaining ontologies, as well as the social processes and technology that support this. Ontogenesis features over 20 articles written by leading academics, and has attracted over 17,000 page reads. Articles are peer-reviewed. Following publication as reviewed, articles are stable and can be cited by stable URL or DOI. Ontogenesis is now archived by the British Library as part of the UK Web Archive and is indexed by Google Scholar. The initial idea for Ontogenesis came from Phillip Lord. You can read the original manifesto that they wrote, describing the purpose of this blog. Ontogenesis is the first and main example of a Knowledgeblog, a flexible and light-weight process for scientific publication. It has received funding from JISC. They are currently open to submissions. Please contact them if you want further information, or would like to offer articles for publication., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | ontology, scientific publication |
is related to: Knowledge Blog has parent organization: Knowledge Blog |
JISC | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144451 | SCR_005380 | 2026-08-12 10:49:09 | 3 | |||||||
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VolumeRover Resource Report Resource Website 1+ mentions |
VolumeRover (RRID:SCR_005457) | VolRover | image processing software, d visualization software, software application, data processing software, software resource | VolumeRover (a.k.a VolRover) is an interactive multi-purpose image processing software that can visualize three dimensional imaging data of any size (as big as terabyte) in a commodity PC or workstation and additionally supports the following image processing operations. Image Contrast Enhancement, Filtering/Noise Reduction, Image Segmentation, Isocontouring, Symmetry Detection (for Virus Maps, Boundary-free Image Skeletonization. VolRover provides a user interface to a number of CVC software packages including Segmentation, Contrast Enhancement, and Motif Elucidation. | image | has parent organization: University of Texas at Austin; Texas; USA | NSF CI-9982297; NSF CCR-9988357; NSF 1018140; NIDCD DC00241 |
PMID:14643216 | nlx_144564 | SCR_005457 | Volume Rover | 2026-08-12 10:49:10 | 2 | ||||||
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becas Resource Report Resource Website 10+ mentions |
becas (RRID:SCR_005337) | service resource, software resource, data access protocol, web service | Web application, API and widget able to recognize and annotate biomedical concepts in text.Provides annotations for isolated, nested and intersected entities.Identifies concepts from multiple semantic groups, providing preferred names and enriching them with references to public knowledge resources. | Annotation, biomedical concept recognition, annotate biomedical concepts, text, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Aveiro; Aveiro; Portugal |
Free, Freely available | biotools:becas, OMICS_01173 | https://bioinformatics.ua.pt/software/becas/, https://bio.tools/becas | SCR_005337 | 2026-08-12 10:49:09 | 12 | ||||||||
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geneXplain Resource Report Resource Website 50+ mentions |
geneXplain (RRID:SCR_005573) | GeneXplain | software toolkit, software application, data processing software, software resource, workflow software | An online toolbox and workflow management system for a broad range of bioinformatic and systems biology applications. The individual modules, or Bricks, are unified under a standardized interface, with a consistent look-and-feel and can flexibly be put together to comprehensive workflows. The workflow management is intuitively handled through a simple drag-and-drop system. With this system, you can edit the predefined workflows or compose your own workflows from scratch. Your own Bricks can easily be added as scripts or plug-ins and can be used in combination with pre-existing analyses. GeneXplain GmbH provides a number of state-of-the-art bricks; some of them can be obtained free of charge, while others require licensing for small fee in order to guarantee active maintenance and dynamic adaptation to the rapidly developing know-how in this field. | scientific workflow, bioinformatics, systems biology, network modeling, microarray, proteomics, mirna, chip-chip, sequence, biomarker, gene expression | nlx_146199 | SCR_005573 | geneXplain GmbH | 2026-08-12 10:49:12 | 73 | |||||||||
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BIIT - Bioinformatics Algorithmics and Data Mining Group Resource Report Resource Website 10+ mentions |
BIIT - Bioinformatics Algorithmics and Data Mining Group (RRID:SCR_005690) | BIIT Research group | portal, data or information resource, department portal, text-mining software, software resource, software application, organization portal | The Bioinformatics, Algorithmics, and Data Mining group BIIT lead by prof. Jaak Vilo is a joint research group between the Department of Computer Science (University of Tartu), Quretec, and the Estonian Biocenter. Our main research topics and capabilities include the gene regulation, gene expression data analysis, biological data mining, systems biology, combinatorial pattern matching, developing software for biomedical research databases, as well as partnering in stem cell and cancer related projects. Software * MEM - Multi-Experiment-Matrix -- large-scale gene expression data queries and mining (Genome Biology 2009) * g:Profiler family of tools for functional assessment of gene groups, gene ID mappings, orthology and expression similarity searches. (NAR web server issue 2007) * KEGGanim - visualisation of high-throughput data on biological pathway charts (Bioinformatics, 2007) * GraphWeb - a tool for mining large biological networks (NAR Web server issue 2008) * FunGenES data atlas * More software tools | gene regulation, gene expression, data analysis, biological, data mining, systems biology, combinatorial pattern matching, software, biomedical research, stem cell, cancer |
has parent organization: University of Tartu; Tartu; Estonia is parent organization of: GraphWeb is parent organization of: g:Profiler |
nlx_149141 | http://biit.cs.ut.ee/about/main | SCR_005690 | BIIT - Bioinformatics Algorithmics Data Mining Group, BIIT Group - Institute of Computer Science | 2026-08-12 10:49:14 | 10 | |||||||
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CIPF Bioinformatics and Genomics Department Resource Report Resource Website 1+ mentions |
CIPF Bioinformatics and Genomics Department (RRID:SCR_005692) | CIPF Bioinformatics and Genomics | portal, data or information resource, institution, department portal, organization portal | Biomedicine can only be understood in the context of genomics and with the concourse of bioinformatics. Our department aims to tackle biomedical problems from a system's biology perspective. Following this, the general objective we seek through the main lines of research is to relate the mutations (Pharmacogenomics and Comparative Genomics) to their effect at cellular and phenotypic level (Functional Genomics) trying to understand the mechanism of action (Structural Genomics). Systems Biology Genes operate within an intricate network of interactions that we have only recently started to envisage. Many higher-order levels of interaction are continuously being discovered. In this scenario we are interested in developing methods and tools which can help to understand large-scale experiments from a systems biology perspective. Comparative genomics We are interested in the analysis of patterns and processes occurred during the evolution of our genome, and in the application of the evolutionary thought in human health and disease. * Adaptive Human Evolution * Evolutionary Pharmacogenetics * SNP's and Human Disease Structural genomics Our Unit aims to develop and apply computational methods for understanding the molecular mechanisms of cell regulation beyond proteins. In particular, we apply our methods to study the interaction of small chemical compounds with proteins and to characterize their molecular actions. We are also developing methods for RNA 3D structure prediction with the aim of applying them to understand the effects of non-coding RNA molecules. Finally, in collaboration with experimentalists, we are working in determining the first ever 3D structure of a genomic domain in human. | genomics, bioinformatics |
has parent organization: Principe Felipe Research Centre; Valencia; Spain is parent organization of: Babelomics |
nlx_149143 | SCR_005692 | CIPF Department of Bioinformatics, CIPF Bioinformatics Genomics | 2026-08-12 10:49:13 | 5 | ||||||||
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NCBO Annotator Resource Report Resource Website 1+ mentions |
NCBO Annotator (RRID:SCR_005329) | NCBO Annotator | service resource, production service resource, data access protocol, software resource, web service | A Web service that annotates textual metadata (e.g. journal abstract) with relevant ontology concepts. NCBO uses this Web service to annotate resources in the NCBO Resource Index. They also provide this Web service as a stand-alone service for users. This Web service can be accessed through BioPortal or used directly in your software. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). Their service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards. | ontology, annotation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: STOP has parent organization: BioPortal has parent organization: National Centers for Biomedical Computing has parent organization: Stanford University; Stanford; California |
NHGRI U54 HG004028 | PMID:19483092 | biotools:bioportal, nlx_144389, OMICS_01172 | https://bio.tools/bioportal | SCR_005329 | Open Biomedical Annotator, NCBO BioPortal Annotator | 2026-08-12 10:49:08 | 6 | |||||
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TAIR Keyword Browser Resource Report Resource Website 10+ mentions |
TAIR Keyword Browser (RRID:SCR_005687) | TAIR Keyword Browser | service resource, data or information resource, production service resource, database, analysis service resource, data analysis service | TAIR Keyword Browser searches and browses for Gene Ontology, TAIR Anatomy, and TAIR Developmental stage terms, and allows you to view term details and relationships among terms. It includes links to genes, publications, microarray experiments and annotations associated with the term or any children terms. Platform: Online tool | gene ontology, gene, publication, microarray, annotation, cellular component, biological process, molecular function, plant, growth, development, stage, anatomical entity, anatomy, ontology, browser, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: TAIR |
Free for academic use | nlx_149132 | http://www.arabidopsis.org/servlets/Search?action=new_search&type=keyword | SCR_005687 | TAIR Keyword Search and Browse, The Arabidopsis Information Resource Keyword Browser | 2026-08-12 10:49:14 | 37 | ||||||
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CoPub Resource Report Resource Website 1+ mentions |
CoPub (RRID:SCR_005327) | CoPub | service resource, software resource, data access protocol, web service | Text mining tool that detects co-occuring biomedical concepts in abstracts from the MedLine literature database. It allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that are significantly correlated with the set of input genes. These lists link to Medline abstracts in which the co-occurring input genes and correlated keywords are highlighted. Furthermore, CoPub can graphically visualize differentially expressed genes and over-represented keywords in a network, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs. | microarray, gene, literature, enrich, annotate, network, database, differential expression, bio.tools |
uses: MEDLINE uses: Gene Ontology is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Netherlands Bioinformatics Centre |
Netherlands Bioinformatics Centre | PMID:18442992 | Free, Public, Acknowledgement requested | OMICS_01178, biotools:copub | https://bio.tools/copub | http://services.nbic.nl/cgi-bin/copub/CoPub.pl | SCR_005327 | 2026-08-12 10:49:08 | 5 | ||||
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Genetic Testing Registry Resource Report Resource Website 10+ mentions |
Genetic Testing Registry (RRID:SCR_005565) | GTR | service resource, data or information resource, database, data repository, storage service resource | Central location for voluntary submission of genetic test information by providers including the test''s purpose, methodology, validity, evidence of the test''s usefulness, and laboratory contacts and credentials. GTR aims to advance the public health and research into the genetic basis of health and disease. GTR is accepting registration of clinical tests for Mendelian disorders, complex tests and arrays, and pharmacogenetic tests. These tests may include multiple methods and may include multiple major method categories such as biochemical, cytogenetic, and molecular tests. GTR is not currently accepting registration of tests for somatic disorders, research tests or direct-to-consumer tests. | genetic, gene, clinical, genetic test, condition, phenotype, disease name, trait, drug, protein, analyte, disease, laboratory, molecular, clinical, genetics, people |
lists: MedGen is listed by: OMICtools has parent organization: NCBI |
The community can contribute to this resource | nlx_144654, OMICS_01541 | SCR_005565 | NIH Genetic Testing Registry, GTR: Genetic Testing Registry | 2026-08-12 10:49:11 | 36 | |||||||
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Pandora - Protein ANnotation Diagram ORiented Analysis Resource Report Resource Website 1+ mentions |
Pandora - Protein ANnotation Diagram ORiented Analysis (RRID:SCR_005686) | Pandora | service resource, production service resource, data or information resource, database, analysis service resource, data analysis service | With PANDORA, you can search for any non-uniform sets of proteins and detect subsets of proteins that share unique biological properties and the intersections of such sets. PANDORA supports GO annotations as well as additional keywords (from UniProt Knowledgebase, InterPro, ENZYME, SCOP etc). It is also integrated into the ProtoNet system, thus allowing testing of thousands of automatically generated protein families. Note that PANDORA replaces the ProtoGO browser developed by the same group. Platform: Online tool | protein, annotation, mass spectrometry, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel |
Israeli Ministry of Defense ; Hebrew University of Jerusalem; Jerusalem; Israel |
PMID:14500825 | Free for academic use | nlx_149131 | SCR_005686 | Protein ANnotation Diagram ORiented Analysis | 2026-08-12 10:49:13 | 2 | |||||
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GoFish Resource Report Resource Website 1+ mentions |
GoFish (RRID:SCR_005682) | GoFish | service resource, production service resource, source code, analysis service resource, software resource, data analysis service | Software program, available as a Java applet online or to download, allows the user to select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, ontology or annotation browser, java, windows, mac os x, linux, unix, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada has parent organization: Harvard Medical School; Massachusetts; USA |
Aventis Pharmaceuticals ; Howard Hughes Medical Institute ; NHGRI |
PMID:12691998 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:gofish, nlx_149126, OMICS_02272 | http://llama.mshri.on.ca/Software.html, https://bio.tools/gofish | SCR_005682 | 2026-08-12 10:49:14 | 1 | |||||
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MINC/Atlases Resource Report Resource Website 1+ mentions |
MINC/Atlases (RRID:SCR_005281) | MINC/Atlases | data or information resource, narrative resource, wiki, atlas, reference atlas | A linear average model atlas produced by the International Consortium for Brain Mapping (ICBM) project. A set of full- brain volumetric images from a normative population specifically for the purposes of generating a model were collected by the Montreal Neurological Institute (MNI), UCLA, and University of Texas Health Science Center at San Antonio Research Imaging Center (RIC). 152 new subjects were scanned using T1, T2 and PD sequences using a specific protocol. These images were acquired at a higher resolution than the original average 305 data and exhibit improved contrast due predominately to advances in imaging technology. Each individual was linearly registered to the average 305 and a new model was formed. In total, three models were created at the MNI, the ICBM152_T1, ICBM152_T2 and ICBM152_PD from 152 normal subjects. This resulting model is now known as the ICBM152 (although the model itself has not been published). One advantage of this model is that it exhibits better contrast and better definition of the top of the brain and the bottom of the cerebellum due to the increased coverage during acquisition. The entirely automatic analysis pipeline of this data also included grey/white matter segmentation via spatial priors. The averaged results of these segmentations formed the first MNI parametric maps of grey and white matter. The maps were never made publicly available in isolation but have formed parts of other packages for some time including SPM, FSL AIR and as models of grey matter for EEG source location in VARETTA and BRAINWAVE. Again, as these models are an approximation of Talairach space, there are differences in varying areas, to continue our use of origin shift as an example, the ICBM models are approximately 152: +3.5mm in Z and +-co-ordinate -3.5mm and 2.0mm in Y as compared to the original Talairach origin. In addition to the standard analysis performed on the ICBM data, 64 of the subjects data were segmented using model based segmentation. 64 of the original 305 were manually outlined and a resulting parametric VOI atlas built. The native data from these acquisitions was 256x256 with 1mm slices. The final image resolution of this data was 181x217x181 with 1mm isotropic voxels. Refer to the ICBM152 NonLinear if you are fitting an individual to model and do not care about left/right comparisons. A short history of the various atlases that have been produced at the BIC (McConnell Brain Imaging Center, Montreal Neurological Institute) is provided. | atlas, brain, template, human, magnetic resonance imaging |
is related to: ICBM 152 Nonlinear atlases version 2009 is related to: McConnell Brain Imaging Center is related to: International Consortium for Brain Mapping is related to: Laboratory of Neuro Imaging is related to: International Consortium for Brain Mapping has parent organization: Wikibooks |
Normal | nlx_144315 | SCR_005281 | MINC / Atlases | 2026-08-12 10:49:08 | 3 | |||||||
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Bisque database Resource Report Resource Website 1+ mentions |
Bisque database (RRID:SCR_005559) | Bisque | service resource, data or information resource, production service resource, image collection, database, image repository, data repository, analysis service resource, storage service resource, data analysis service | Open source database for exchange and exploration of biological images. Used to store, visualize, organize and analyze images in cloud. Centered around database of images and metadata. | microscopy, cell, mouse, confocal, medical, biology, hippocampus, macular degeneration, maize, microtubule, plant, retina |
has parent organization: Center for Bio-Image Informatics has parent organization: University of California at Santa Barbara; California; USA |
NSF Information Technology Research ; NSF infrastructure awards ; iPlant Collaborative ; NSF ITR-0331697; NSF IIS-0808772 |
PMID:20031971 | Restricted | SCR_008430, nlx_144652, nif-0000-30205 | http://bisque.ece.ucsb.edu/client_service/ | SCR_005559 | Bisque Image Repository, Bio-Image Semantic Query User Environment, Bio-Image Semantic Query User Environment database, Bio-Image Semantic Query User Environment Database | 2026-08-12 10:49:12 | 5 | ||||
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MAKER Web Annotation Service Resource Report Resource Website 1+ mentions |
MAKER Web Annotation Service (RRID:SCR_005318) | MWAS | service resource, production service resource, data access protocol, software resource, web service | The MAKER Web Annotation Service (MWAS) is an easily configurable web-accessible genome annotation pipeline. It''''s purpose is to allow research groups with small to intermediate amounts of eukaryotic and prokaryotic genome sequence (i.e. BAC clones, small whole genomes, preliminary sequencing data, etc.) to independently annotate and analyze their data and produce output that can be loaded into a genome database. MWAS is build on the stand alone genome annotation pipeline MAKER, and users who wish to annotate larger datasets and whole genomes are free to download MAKER for use on their own systems. MWAS identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MWAS can also automatically train popular gene prediction algorithms for use on new genomes for which pre-existing information is limited. MAKER is a member of the Generic Model Organism Database (GMOD) project and output produced by this site can be directly used with other GMOD tools. Annotations can be directly viewed online by the user via GBrowse, JBrowse, and Apollo, or they can be downloaded for local analysis and integration into a genome database. MWAS also supplies summary statistics on sequence features via the Sequence Ontology tool SOBA. MWAS should prove especially useful for emerging model organism genome projects with minimal bioinformatics expertise and computer resources, since a user can produce final genome annotations without having to install and configure any software locally. | data management, human genome map, genome annotation, annotation, curation, genome, sequence |
is related to: MAKER has parent organization: University of Utah; Utah; USA |
nlx_144374 | SCR_005318 | 2026-08-12 10:49:09 | 7 | |||||||||
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ADHD-200 Sample Resource Report Resource Website 10+ mentions |
ADHD-200 Sample (RRID:SCR_005358) | ADHD-200, | portal, data or information resource, disease-related portal, data set, topical portal | A grassroots initiative dedicated to accelerating the scientific community''''s understanding of the neural basis of ADHD through the implementation of open data-sharing and discovery-based science. They believe that a community-wide effort focused on advancing functional and structural imaging examinations of the developing brain will accelerate the rate at which neuroscience can inform clinical practice. The ADHD-200 Global Competition invited participants to develop diagnostic classification tools for ADHD diagnosis based on functional and structural magnetic resonance imaging (MRI) of the brain. Applying their tools, participants provided diagnostic labels for previously unlabeled datasets. The competition assessed diagnostic accuracy of each submission and invited research papers describing novel, neuroscientific ideas related to ADHD diagnosis. Twenty-one international teams, from a mix of disciplines, including statistics, mathematics, and computer science, submitted diagnostic labels, with some trying their hand at imaging analysis and psychiatric diagnosis for the first time. The data for the competition was provided by the ADHD-200 Consortium. Consortium members from institutions around the world provided de-identified, HIPAA compliant imaging datasets from almost 800 children with and without ADHD. A phenotypic file including all of the test set subjects and their diagnostic codes can be downloaded. Winner is presented. The ADHD-200 consortium included: * Brown University, Providence, RI, USA (Brown) * The Kennedy Krieger Institute, Baltimore, MD, USA (KKI) * The Donders Institute, Nijmegen, The Netherlands (NeuroImage) * New York University Medical Center, New York, NY, USA (NYU) * Oregon Health and Science University, Portland, OR, USA (OHSU) * Peking University, Beijing, P.R.China (Peking 1-3) * The University of Pittsburgh, Pittsburgh, PA, USA (Pittsburgh) * Washington University in St. Louis, St. Louis, MO, USA (WashU) | mri, fmri, brain, neuroimaging, attention deficit-hyperactivity disorder, anatomical, resting state functional mri, child, adolescent, human, young, early adult human, functional imaging, structural imaging, normal, normal control |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Neuro Bureau has parent organization: 1000 Functional Connectomes Project is parent organization of: ADHD-200 Preprocessed Data |
Attention deficit-hyperactivity disorder | Account required, Acknowledgement requested, Non-commercial | nlx_144426 | SCR_005358 | ADHD-200 Consortium | 2026-08-12 10:49:09 | 20 | ||||||
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CBRAIN Resource Report Resource Website 10+ mentions |
CBRAIN (RRID:SCR_005513) | CBRAIN | service resource, production service resource, software resource, analysis service resource, storage service resource, data analysis service | A flexible software platform for distributed processing, analysis, exchange and visualization of brain imaging data. The expected result is a middleware platform that will render the processing environment (hardware, operating systems, storage servers, etc...) transparent to a remote user. Interaction with a standard web browser allows application of complex algorithm pipelines to large datasets stored at remote locations using a mixture of network available resources such as small clusters, neuroimaging tools and databases as well as Compute Canada's High Performance Computing Centers (HPC). Though the focus of CBRAIN is providing tools for use by brain imaging researchers, the platform is generalizable to other imaging domains, such as radiology, surgical planning and heart imaging, with profound consequences for Canadian medical research. CBRAIN expanded its concept to include international partners in the US, Germany and Korea. As of December 2010, GBRAIN has made significant progress with the original three partners and has developed new partners in Singapore, China, India, and Latin America. CBRAIN is currently deployed on 6 Compute Canada HPC clusters, one German HPC cluster and 3 clusters local to McGill University Campus, totaling more than 80,000 potential CPU cores. | brain, neuroimaging, imaging, middleware, platform, network, data sharing, web application, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McGill University; Montreal; Canada is parent organization of: Latin American Brain Mapping Network (LABMAN) |
Free | nlx_144612 | http://www.nitrc.org/projects/cbrain | SCR_005513 | 2026-08-12 10:49:10 | 30 | |||||||
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PRIMEGENS Resource Report Resource Website 1+ mentions |
PRIMEGENS (RRID:SCR_005474) | PRIMEGENS | service resource, production service resource, analysis service resource, software resource, data analysis service | A Web-based Tool for High-throughput Primer and Probe Design. The program has its different utilities available on its web server. A standalone version is also available. Algorithms: * SSPD - Sequence Specific Primer Design: to design primers for each of the specific sequences given by the user in the query input file against any alternate potential hybridization with any of the sequences given in the database input file. * PSPD - Probe Specific Primer Design: to design primers it selects the gene-specific fragments (probes) to design primer pairs for their PCR amplification. * FSPD Fragment Specific Primer Design: primer design algorithm used when there is a very long query sequence for which multiple primers are required for its amplification. * Check Binding Specificity * Probe Design Only: Probe design algorithm could be used to find sequence-specific probes, which doesn''t show any blast hit against database. Such probe design has been used for targeted sequencing like agilent sure-select technology with next-generation sequencing. | primer design, high-throughput primer, probe, microarray, analysis, blast, hybridization, primer, probe design, dna methylation |
is listed by: OMICtools has parent organization: University of Missouri; Missouri; USA |
DOE ; DOD ; NIH |
PMID:21415011 PMID:18579568 PMID:17951795 PMID:12424113 |
Free for academic use, Commercial use requires license | OMICS_00637, OMICS_02346 | http://digbio.missouri.edu/primegens/ | SCR_005474 | PRIMEGENS-w3, PRIMEGENS - High-throughput Primer and Probe Design, PRIMEGENSw3 | 2026-08-12 10:49:10 | 3 | ||||
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Bowtie Resource Report Resource Website 10000+ mentions |
Bowtie (RRID:SCR_005476) | sequence analysis software, image analysis software, software resource, software application, data processing software, alignment software, data analysis software | Software ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner. | sequence, analysis, long, reference, read, alignment, gap, local, pair, end, rna, rnaseq, bio.tools |
is used by: deFuse is used by: Short Read Sequence Typing for Bacterial Pathogens is used by: TopHat is used by: BS Seeker is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Bowtie 2 has parent organization: Johns Hopkins University; Maryland; USA is required by: RelocaTE |
NHGRI R01 HG006102; NIGMS R01 GM083873; Amazon Web Services in Education Research |
PMID:19261174 DOI:10.1186/gb-2009-10-3-r25 |
Free, Available for download, Freely available | biotools:bowtie, OMICS_00653 | https://github.com/BenLangmead/bowtie, https://bio.tools/bowtie, https://sources.debian.org/src/bowtie/ | SCR_005476 | 2026-08-12 10:49:10 | 13799 | ||||||
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MicrobesOnline Resource Report Resource Website 100+ mentions |
MicrobesOnline (RRID:SCR_005507) | MicrobesOnline | service resource, data or information resource, production service resource, database, source code, analysis service resource, software resource, data analysis service | MicrobesOnline is designed specifically to facilitate comparative studies on prokaryotic genomes. It is an entry point for operon, regulons, cis-regulatory and network predictions based on comparative analysis of genomes. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html. | microbe, genome, bacteria, archaea, fungi, prokaryote, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: Lawrence Berkeley National Laboratory |
DOE DE-AC02-05CH11231 | PMID:19906701 | nlx_144607, biotools:microbesonline | https://bio.tools/microbesonline | SCR_005507 | Microbial Genomics Database, Microbes Online | 2026-08-12 10:49:10 | 166 |
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