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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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tRNAscan-SE Resource Report Resource Website 1000+ mentions |
tRNAscan-SE (RRID:SCR_008637) | software resource, service resource, production service resource, data analysis service, web application, analysis service resource | Web server to search for tRNA genes in genomic sequence. If you would like to run tRNAscan-SE locally, you can get the UNIX source code (gzip''d tar file). | bio.tools, tRNA genes, genomic sequence |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools has parent organization: University of California at Santa Cruz; California; USA |
PMID:15980563 PMID:9023104 DOI:10.1093/nar/25.5.0955 |
Free, Freely available | SCR_010835, OMICS_00385, nif-0000-32031, biotools:trnascan-se | https://bio.tools/trnascan-se, https://sources.debian.org/src/trnascan-se/ | SCR_008637 | Lowe Lab tRNAscan-SE | 2026-08-06 09:27:15 | 2493 | ||||||
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Vienna RNA Resource Report Resource Website 100+ mentions |
Vienna RNA (RRID:SCR_008550) | database, data or information resource, software resource | This server provides programs, web services, and databases, related to our work on RNA secondary structures. For general information and other offerings from our group see the main TBI web server. With the 1st of May 2009 we updated our servers to the Vienna RNA package version 1.8.2! The Vienna RNA Servers: * RNAfold server predicts minimum free energy structures and base pair probabilities from single RNA or DNA sequences. * RNAalifold server predicts consensus secondary structures from an alignment of several related RNA or DNA sequences. You need to upload an alignment. * RNAinverse server allows you to design RNA sequences for any desired target secondary structure. * RNAcofold server allows you to predict the secondary structure of a dimer. * RNAup server allows you to predict the accessibility of a target region. * LocARNA server generates structural alignments from a set of sequences. In collaboration with the Bioinformatics Group Freiburg. * barriers server allows you to get insights into RNA folding kinetics. * RNAz server will assist you in detecting thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments. * Structure conservation analysis server will assist you in detecting evolutionarily conserved RNA secondary structures in multiple sequence alignments. * RNAstrand server allows you to predict the reading direction of evolutionarily conserved RNA secondary structures. * RNAxs server assists you in siRNA design. * Bcheck predicts rnpB genes Downloads Get the Source code for: * the Vienna RNA Package, our basic RNA secondary structure analysis software. * The ALIDOT package for finding conserved structure motifs (add-on) * The barriers program for analysis of RNA folding landscapes. Databases * Atlas of conserved Viral RNA Structures found by ALIDOT | bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: ANNOgesic has parent organization: University of Vienna; Vienna; Austria |
DOI:10.1186/1748-7188-6-26 | biotools:vienna_rna_package, nif-0000-31411, OMICS_09351 | https://bio.tools/vienna_rna_package, https://sources.debian.org/src/vienna-rna/ | SCR_008550 | Vienna RNA | 2026-08-06 09:27:10 | 404 | |||||||
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Eukaryote Genes Resource Report Resource Website 10+ mentions |
Eukaryote Genes (RRID:SCR_008617) | database, data or information resource | Provides summary of gene and genomic information from eukaryotic organism databases. This includes gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information, links to extended gene information. | eukaryote, eukaryotic gene ontology, eukaryotic genome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Indiana University; Indiana; USA |
Indiana University Center for Genomics and Bioinformatics ; NSF DBI 0090782; NSF DBI 9982851 |
Free, Freely available | nif-0000-31969, biotools:eugenes, SCR_013197, nif-0000-02818 | https://bio.tools/eugenes | SCR_008617 | euGenes | 2026-08-06 09:27:15 | 17 | ||||||
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Gene Set Enrichment Analysis Resource Report Resource Website 10000+ mentions |
Gene Set Enrichment Analysis (RRID:SCR_003199) | GSEA | software resource, data analysis software, software toolkit, data processing software, software application | Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes. | gene, expression, profile, pathway, data, set, phenotype, genome, enrichment, RNA, analysis, bio.tools, bio.tools |
is used by: Molecular Signatures Database is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GoMapMan has parent organization: Broad Institute |
NCI ; NIH ; NIGMS |
PMID:16199517 | Free, Freely available | nif-0000-30629, SCR_016882, biotools:gsea, OMICS_02279 | http://www.broad.mit.edu/gsea, https://bio.tools/gsea | SCR_003199 | GSEA, Gene Set Enrichment Analysis, Gene Set Enrichment Analysis (GSEA) | 2026-08-06 09:25:49 | 18865 | ||||
|
MAGE-TAB Resource Report Resource Website 1+ mentions |
MAGE-TAB (RRID:SCR_003222) | MAGE-TAB | standard specification, narrative resource, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2023. A simple tab-delimited, spreadsheet-based format which will become a part of the MAGE microarray data standard that can be used for annotating and communicating microarray data in a MIAME compliant fashion. MAGE-TAB will enable laboratories without bioinformatics experience or support to manage, exchange and submit well-annotated microarray data in a standard format using a spreadsheet. The MAGE-TAB format is self-contained, and does not require an understanding of MAGE-ML or XML. | microarray, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: MIAME is related to: DDBJ Omics Archive is related to: ArrayExpress is related to: caArray has parent organization: MAGE |
PMID:17087822 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157259, biotools:tab2mage | https://bio.tools/tab2mage | SCR_003222 | 2026-08-06 09:25:49 | 5 | ||||||
|
Stacks Resource Report Resource Website 500+ mentions |
Stacks (RRID:SCR_003184) | Stacks | data analysis software, software application, software resource, data processing software | A software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. It was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. | population genomics, genetic map, phylogenetics, genetics, next-generation sequencing, rad-seq, genotype-by-sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Oregon; Oregon; USA |
PMID:23701397 PMID:22384329 DOI:10.1111/mec.12354 |
Free, Available for download, Freely available | OMICS_01567, biotools:stacks | https://bio.tools/stacks, https://sources.debian.org/src/stacks/ | SCR_003184 | 2026-08-06 09:25:49 | 623 | ||||||
|
RNAhybrid Resource Report Resource Website 100+ mentions |
RNAhybrid (RRID:SCR_003252) | RNAhybrid | software resource, service resource, production service resource, data analysis service, analysis service resource | Software tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, i.e., the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction. | microrna, target prediction, free energy, rna, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:15383676 DOI:10.1261/rna.5248604 |
Free, Available for download, Freely available | OMICS_00416, biotools:rnahybrid, nif-0000-31412 | https://bio.tools/rnahybrid, https://sources.debian.org/src/rnahybrid/ | SCR_003252 | 2026-08-06 09:25:50 | 477 | ||||||
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Weighted Gene Co-expression Network Analysis Resource Report Resource Website 1000+ mentions |
Weighted Gene Co-expression Network Analysis (RRID:SCR_003302) | WGCNA | data analysis software, software application, software resource, data processing software | Software R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, co-expression, analysis, network, bio.tools, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of California at Los Angeles; California; USA |
NCI P50CA092131; NIDA 1R01DA030913-01; NIDCR R01DE019255; NIAID U19 AI063603-01 |
PMID:19114008 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31889, biotools:crosslinkwgcna | http://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/Rpackages/WGCNA/#citation, https://bio.tools/crosslinkwgcna | SCR_003302 | WGCNA: an R package for weighted correlation network analysis | 2026-08-06 09:25:51 | 1860 | ||||
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QGene Resource Report Resource Website 100+ mentions |
QGene (RRID:SCR_003209) | QGene | source code, software resource, data analysis software, data processing software, software application, simulation software | A free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request. | gene, genetic, genomic, java, qtl mapping, trait analysis, trait, population, simulation, map, quantitative trait locus, comparison, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Kansas State University; Kansas; USA |
NSF DBI 0109879; USDA-NRI Applied Plant Genomics Program 2004-35317-14867 |
PMID:18940826 | Free, Available for download, Freely available | biotools:qgene, nif-0000-31383 | https://bio.tools/qgene | http://coding.plantpath.ksu.edu/qgene | SCR_003209 | QGene - Software for QTL data exploration | 2026-08-06 09:25:49 | 126 | |||
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Xenbase Resource Report Resource Website 100+ mentions |
Xenbase (RRID:SCR_003280) | XenBase | storage service resource, service resource, data repository, data or information resource, image repository, database | Data collection for Xenopus laevis and Xenopus tropicalis biology and genomics. | molecular neuroanatomy resource, dna target, protein target, gene, genome, function, sequence, orthology, publication, gene expression, model organism, genomics, development, annotation, blast, development stage, publication, in situ hybridization, immunohistochemistry, video resource, organism-related portal, experimental protocol, organism supplier, data analysis service, developmental stage, gold standard, bio.tools, FASEB list, RRID Community Authority |
is listed by: OMICtools is listed by: One Mind Biospecimen Bank Listing is listed by: bio.tools is listed by: Debian is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: University of Calgary; Alberta; Canada is parent organization of: Xenopus Anatomy Ontology |
NICHD R01 HD045776; NICHD P41 HD064556 |
PMID:23125366 PMID:19884130 PMID:36755307 |
Free, Available for download, Freely available | biotools:xenbase, OMICS_01665, nif-0000-01286, r3d100010279 | http://www.xenbase.org/entry/, https://bio.tools/xenbase, https://doi.org/10.17616/R3MP4S | SCR_003280 | Xenbase: Xenopus laevis and tropicalis biology and genomics resource | 2026-08-06 09:25:50 | 446 | ||||
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PLANTTFDB Resource Report Resource Website 1000+ mentions |
PLANTTFDB (RRID:SCR_003362) | PlantTFDB | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | Comprehensive plant transcription factor database. Interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis.PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors | transcription factor, expression, regulation, interaction, conserved element, phenotype, function, evolution, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Database of Poplar Transcription Factors is related to: Plant Ontology has parent organization: Peking University; Beijing; China |
China 863 ; China 973 ; NSFC ; China NSFC |
PMID:24174544 PMID:17933783 PMID:21097470 |
Free, Available for download, Freely available | nif-0000-03311, biotools:planttfdb_2.0, OMICS_00560, r3d100010137 | https://bio.tools/planttfdb_2.0, https://doi.org/10.17616/R3JG6V | http://planttfdb.cbi.pku.edu.cn | SCR_003362 | , PlantTFDB 2.0, Plant Transcription Factor Database | 2026-08-06 09:25:52 | 1109 | |||
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genomation Resource Report Resource Website 50+ mentions |
genomation (RRID:SCR_003435) | genomation | software resource, data analysis software, software toolkit, data processing software, software application | Software R package for simplfiying common tasks in genomic feature analysis. Toolkit to summarize, annotate and visualize genomic intervals. Provides functions for reading BED and GFF files as GRanges objects, summarizing genomic features over predefined windows so users can make average enrichment of features over defined regions or produce heatmaps. Can annotate given regions with other genomic features such as exons,introns and promoters. | genome, genomic interval, genomic feature analysis, GRanges objects, annotate given regions, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:25417204 | Free, Available for download, Freely available | biotools:genomation, OMICS_02306 | https://github.com/al2na/genomation, https://github.com/BIMSBbioinfo/genomation, https://bio.tools/genomation | http://al2na.github.io/genomation/ | SCR_003435 | 2026-08-06 09:25:53 | 58 | |||||
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NeuroMatic Resource Report Resource Website 100+ mentions |
NeuroMatic (RRID:SCR_004186) | data analysis software, software application, software resource, data processing software | NeuroMatic is a collection of Igor Pro functions for analyzing electrophysiological data. By allowing users to organize their data into Sets and Groups, NeuroMatic makes it relatively easy to compute transformations and statistical analyses on their data, including scaling, alignment averaging, baseline subtraction, spike detection, stationarity analysis, rise-time computations, etc. Being open source and modular designed, NeuroMatic also allows users to develop their own analysis functions that can be easily incorporated into NeuroMatic's framework. Note, if you have reached this page in search of a freeware tool for neuronal reconstructions, you are more likely to be interested in Neuromantic, a software package that sounds like NeuroMatic, but is not quite the same. Features of NeuroMatic Include * Sorting, Scaling, Averaging, Interpolation * Max / Min / Mean / Level / Rise Time / FWHM / Slope Measurements * Stability / Stationarity Analysis * Event Detection * Waveform Template Matching * Spike Raster Plots * Interspike-Interval and Peri-Stimulus Time (PST) Histograms * Compact Easy-to-Use Interface * Modular design as a basis for your own procedures * Extra space for your own buttons and controls * Import functions for Axograph and Pclamp data * Automatic macro generation for batch processing Supporting Agencies: MRC, Wellcome Trust Spike, Event, Fit, NClamp, Acquisition, spike train, EPSP, IPSP, IPSC, EPSC | epsc, epsp, event, fit, acquisition, data management, ipsc, ipsp, nclamp, software, spike, spike train, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University College London; London; United Kingdom |
PMID:29670519 | nif-0000-00073, biotools:neuromatic | https://bio.tools/neuromatic | SCR_004186 | NeuroMatic | 2026-08-06 09:26:03 | 301 | |||||||
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bioRxiv Resource Report Resource Website 1000+ mentions |
bioRxiv (RRID:SCR_003933) | bioRxiv | portal, community building portal, database, data or information resource | A free archive and distribution service for unpublished preprints in the life sciences allowing authors to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals. An article may be posted prior to, or concurrently with, submission to a journal but should not be posted if it has already been published. Once an article is published in a journal, bioRxiv will update the preprint with a link to the published version. | preprint, life science, bio.tools, FASEB list |
is used by: PrePubMed is listed by: LabWorm is listed by: bio.tools is listed by: Debian is related to: Overleaf has parent organization: Cold Spring Harbor Laboratory |
Free, Acknowledgement requested, The community can contribute to this resource | nlx_158302, biotools:bioRxiv | https://bio.tools/bioRxiv | SCR_003933 | bioRxiv - the preprint server for biology | 2026-08-06 09:26:02 | 1246 | ||||||
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Git Resource Report Resource Website 50+ mentions |
Git (RRID:SCR_003932) | software application, version source control system, software development tool, software resource | A free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. Git is easy to learn and has a tiny footprint with lightning fast performance. It outclasses SCM tools like Subversion, CVS, Perforce, and ClearCase with features like cheap local branching, convenient staging areas, and multiple workflows. | version control, distributed, bio.tools |
is used by: DataLad is used by: G-Node Data Infrastructure Services is listed by: bio.tools is listed by: Debian works with: git-annex |
GNU General Public License, v2 | nlx_158301, biotools:Git | https://bio.tools/Git | SCR_003932 | 2026-08-06 09:26:00 | 66 | ||||||||
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PubChem Resource Report Resource Website 10000+ mentions |
PubChem (RRID:SCR_004284) | storage service resource, service resource, data repository, data or information resource, database | Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI). | collection, information, data, chemical, structure, biological, property, small, molecule, siRNA reagent, bio.tools |
uses: ChEMBL is used by: NIF Data Federation is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: GEROprotectors is listed by: OMICtools is listed by: re3data.org is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: NCBI Structure is related to: Molecular Libraries Program is related to: NIH Data Sharing Repositories is related to: PubChem BioAssay has parent organization: NCBI is parent organization of: PubChem Substance works with: MiMeDB |
NLM | PMID:21418625 PMID:21272340 PMID:20970519 PMID:20298522 PMID:19825798 |
Free, Freely Available | biotools:pubchem, nlx_42691, nlx_29861, r3d100010538, OMICS_01587 | https://bio.tools/pubchem, https://doi.org/10.17616/R3GW37 | SCR_004284 | 2026-08-06 09:26:05 | 13540 | ||||||
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PDBe - Protein Data Bank in Europe Resource Report Resource Website 50+ mentions |
PDBe - Protein Data Bank in Europe (RRID:SCR_004312) | PDBe | storage service resource, service resource, data repository, data or information resource, database | The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules. | x-ray, nmr, cryo-em, hybrid method, dna, protein, rna, sugar, ligand, virus, compound, fold, enzyme, 3d spatial image, structure, macromolecule, protein-protein interaction, gold standard, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: DNA DataBank of Japan (DDBJ) is related to: EMDataResource.org is related to: Worldwide Protein Data Bank (wwPDB) is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: DNA DataBank of Japan (DDBJ) is related to: Worldwide Protein Data Bank (wwPDB) is related to: PDBj - Protein Data Bank Japan is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: European Bioinformatics Institute is parent organization of: Electron Microscopy Data Bank at PDBe (MSD-EBI) works with: MOLEonline |
European Molecular Biology Laboratory; Heidelberg; Germany ; Wellcome Trust ; BBSRC ; NIH ; European Union ; MRC ; CCP4 |
PMID:21045060 PMID:21460450 PMID:19858099 |
r3d100012791, biotools:pdbe, nlx_32372 | https://bio.tools/pdbe, https://doi.org/10.17616/R3J226 | SCR_004312 | Protein DataBank Europe, Protein DataBank in Europe, PDBe, Protein Data Bank in Europe, Protein Data Bank Europe, Macromolecular Structure Database | 2026-08-06 09:26:05 | 52 | |||||
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Stem Cell Discovery Engine Resource Report Resource Website 50+ mentions |
Stem Cell Discovery Engine (RRID:SCR_004453) | SCDE | storage service resource, source code, software resource, service resource, production service resource, data repository, data or information resource, analysis service resource, database | An online database of curated cancer stem cell (CSC) experiments coupled to the Galaxy analytical framework. Driven by a need to improve our understanding of molecular processes that are common and unique across cancer stem cells (CSCs), the SCDE allows users to consistently describe, share and compare CSC data at the gene and pathway level. The initial focus has been on carefully curating tissue and cancer stem cell-related experiments from blood, intestine and brain to create a high quality resource containing 53 public studies and 1098 assays. The experimental information is captured and stored in the multi-omics Investigation/Study/Assay (ISA-Tab) format and can be queried in the data repository. A linked Galaxy framework provides a comprehensive, flexible environment populated with novel tools for gene list comparisons against molecular signatures in GeneSigDB and MSigDB, curated experiments in the SCDE and pathways in WikiPathways. Investigation/Study/Assay (ISA) infrastructure is the first general-purpose format and freely available desktop software suite targeted to experimentalists, curators and developers and that: * assists in the reporting and local management of experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) from studies employing one or a combination of technologies; * empowers users to uptake community-defined minimum information checklists and ontologies, where required; * formats studies for submission to a growing number of international public repositories endorsing the tools, currently ENA (genomics), PRIDE (proteomics) and ArrayExpress (transcriptomics). Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples and much much more. Best of all, Galaxy''''s history system provides a complete analyses record that can be shared. Every history is an analysis workflow, which can be used to reproduce the entire experiment. The code for this Galaxy instance is available for download from BitBucket. | stem cell, analysis, cancer stem cell, galaxy, gene, pathway, molecular signature, tissue, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Galaxy is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Harvard T.H. Chan School of Public Health |
Cancer | NCI 1RC2CA148222-01 | PMID:22121217 | Free, The community can contribute to this resource | biotools:scde_discovery, nlx_44656 | https://bio.tools/scde_discovery | SCR_004453 | Harvard Stem Cell Discovery Engine, SCDE - Stem Cell Discovery Engine | 2026-08-06 09:26:08 | 57 | |||
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RatMine Resource Report Resource Website 1+ mentions |
RatMine (RRID:SCR_004190) | software resource, service resource, data access protocol, production service resource, data analysis service, data or information resource, web service, analysis service resource, database | RatMine integrates data from RGD, UniProtKB, NCBI, KEGG and other sources to form a web-based data warehouse and tool set tailored for rat based data research. Search RatMine by entering names, identifiers, or keywords for genes, proteins, pathways, papers, etc. Additionally, we support programmatic access to our data through Application Programming Interface - choose from Perl or Java API. RatMine is a data warehouse that integrates many diverse biological data sets. The main focus is R. norvegicus genomics and proteomics. By integrating such data into one place it is possible to construct queries across domains of biological knowledge. The RatMine user interface is designed to go beyond simply looking up an identifier and viewing a report page. Some of the features include: * Quick Search is available just like on other sites, type in an identifier to see a report page. * Template queries are ''canned'' queries that provide a simple form to perform a specific task. You can create your own templates if you log in. * Lists lets you operate on whole lists of data at once. You can upload lists or save them from results tables. We also create useful public lists for everyone to use. * MyMine lets you create an account to save your own queries, bags and templates, as well as marking public templates as favorites. | disease, interaction, proteins, single nucleotide, gene ontology, mammalian phenotype, publication, genomics, pathway, quantitative trait loci, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Medical College of Wisconsin; Wisconsin; USA |
biotools:RatMine, nlx_21635 | https://bio.tools/RatMine | SCR_004190 | 2026-08-06 09:26:03 | 5 | |||||||||
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RepeatFiller Resource Report Resource Website 10+ mentions |
RepeatFiller (RRID:SCR_017414) | software resource, image analysis software, alignment software, data processing software, software application | Software tool to incorporate newly detected repeat overlapping alignments into pairwise alignment chains. It only aligns local genomic regions that are bounded by colinear aligning blocks, as provided in chains, which makes it feasible to consider all seeds including those that overlap repetitive regions. Used to improve genome alignments by incorporating previously undetected local alignments between repetitive sequences. | Repeat, overlapping, alignment, pairwise, chain, local, genomic, region, colinear, block, sequence, undetected, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany |
DOI:10.1101/696922 | Free, Freely available | biotools:RepeatFiller, BioTools:RepeatFiller | https://bio.tools/RepeatFiller, https://bio.tools/RepeatFiller, https://bio.tools/RepeatFiller | SCR_017414 | 2026-08-06 09:29:04 | 15 |
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