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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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International HapMap Project Resource Report Resource Website 5000+ mentions |
International HapMap Project (RRID:SCR_002846) | HapMap | narrative resource, data or information resource, experimental protocol, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project. | genetic variant, disease, genetic sequence, genetic variation, single nucleotide polymorphism, genetic diversity, dna, sequence, catalog, genome, chromosome, bio.tools |
is used by: BioSample Database at EBI is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SNAP - SNP Annotation and Proxy Search is related to: Haploview is related to: NHGRI Sample Repository for Human Genetic Research is related to: DistiLD - Diseases and Traits in LD is related to: SNP at Ethnos is related to: GBrowse is related to: Broad Institute Genomics Platform has parent organization: NCBI |
Chinese Academy of Sciences ; Chinese Ministry of Science and Technology ; Delores Dore Eccles Foundation ; Genome Canada ; Genome Quebec ; Hong Kong Innovation and Technology Commission ; Japanese Ministry of Education Culture Sports Science and Technology MEXT ; National Natural Science Foundation of China ; SNP Consortium ; University Grants Committee of Hong Kong ; Wellcome Trust ; W. M. Keck Foundation ; NIH |
PMID:14685227 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02940, biotools:int_hapmap_project, r3d100011835, OMICS_00273 | http://www.hapmap.org/, https://bio.tools/int_hapmap_project, https://doi.org/10.17616/R3H06Q | http://snp.cshl.org | SCR_002846 | HapMap Project | 2026-08-03 09:32:03 | 6817 | |||
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Clustal W2 Resource Report Resource Website 5000+ mentions |
Clustal W2 (RRID:SCR_002909) | alignment software, software application, data processing software, image analysis software, service resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. Command line version of multiple sequence alignment program Clustal for DNA or proteins. Alignment is progressive and considers sequence redundancy. No longer being maintained. Please consider using Clustal Omega instead which accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/ClustalW, GCG/MSF, RSF. | multiple, sequence, alignment, cladogram, phylogram, evolution, phylogenetic, tree, protein, nucleic, acid, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: Clustal Omega is related to: UniProt is related to: Clustal Omega is related to: VectorBase is related to: TopoSNP is related to: Clustal 2 has parent organization: European Bioinformatics Institute has parent organization: University College Dublin; Dublin; Ireland |
Science Foundation Ireland | PMID:17846036 PMID:20439314 DOI:10.1093/bioinformatics/btm404 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02562, nif-0000-30076 | http://www.ch.embnet.org/software/ClustalW.html, https://sources.debian.org/src/clustalx/ | http://www.ebi.ac.uk/tools/clustalw/ | SCR_002909 | European Bioinformatics Institute - ClustalW2 | 2026-08-03 09:32:10 | 7830 | ||||
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MIPE Resource Report Resource Website 10+ mentions |
MIPE (RRID:SCR_003065) | standard specification, interchange format, narrative resource, data or information resource, software resource | A XML format that enables genomics researchers to store critical information on PCR experiments. Accompagnying perl scripts are written to read from (dbSTS) or write to a MIPE XML file. | standalone software, pcr, xml, data storage, data exchange |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02358 | http://mipe.sourceforge.net/, https://sources.debian.org/src/mipe/ | SCR_003065 | Minimal Information for PCR Experiments | 2026-08-03 09:32:11 | 31 | |||||||
|
Stacks Resource Report Resource Website 500+ mentions |
Stacks (RRID:SCR_003184) | Stacks | software resource, data processing software, software application, data analysis 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 | 2026-08-03 09:32:14 | 623 | ||||||
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PubChem Resource Report Resource Website 10000+ mentions |
PubChem (RRID:SCR_004284) | data repository, data or information resource, database, storage service resource, service resource | 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 | 2026-08-03 09:32:38 | 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 | data repository, data or information resource, database, storage service resource, service resource | 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 | 2026-08-03 09:32:38 | 52 | |||||
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Stem Cell Discovery Engine Resource Report Resource Website 50+ mentions |
Stem Cell Discovery Engine (RRID:SCR_004453) | SCDE | data repository, production service resource, service resource, database, source code, storage service resource, analysis service resource, data or information resource, software resource | 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 | 2026-08-03 09:32:33 | 57 | |||
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Tree and reticulogram REConstruction Resource Report Resource Website 10+ mentions |
Tree and reticulogram REConstruction (RRID:SCR_004497) | T-REX | production service resource, data analysis service, analysis service resource, service resource, software resource | A web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events. | phylogenetic tree, analysis, visualization, network, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Quebec in Montreal; Quebec; Canada |
PMID:22675075 | biotools:t-rex, OMICS_04264 | https://bio.tools/t-rex | SCR_004497 | Trex-online | 2026-08-03 09:32:34 | 32 | ||||||
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DER Finder Resource Report Resource Website 1+ mentions |
DER Finder (RRID:SCR_004250) | DER Finder | software toolkit, software application, data processing software, software library, software resource | R package for differential expression analysis of RNA-seq data. | differential expression, rna-seq, false discovery rate, genomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24398039 | Free, Public | biotools:derfinder, OMICS_02208 | https://bio.tools/derfinder | SCR_004250 | derfinder | 2026-08-03 09:32:26 | 5 | |||||
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Transporter Classification Database Resource Report Resource Website 100+ mentions |
Transporter Classification Database (RRID:SCR_004490) | TCDB, TC | data repository, production service resource, data analysis service, service resource, software application, data processing software, database, data analysis software, source code, storage service resource, analysis service resource, data or information resource, software resource | Curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from variety of living organisms based on IUBMB-approved transporter classification (TC) system. Descriptions, TC numbers, and examples of over 600 families of transport proteins are provided. TC system is analogous to Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information. TCDB users may submit their own sequenced proteins and descriptions for inclusion into database. The software tools used are all freely available for download. These programs are used for analysis of Protein and DNA sequences. Programs require UNIX server to run. | membrane transport, protein sequence, transporter, bio.tools, FASEB list |
is recommended by: National Library of Medicine is listed by: bio.tools is listed by: Debian has parent organization: University of California at San Diego; California; USA |
NIGMS GM1077402 | PMID:19022853 PMID:16381841 |
Free, Freely available | nlx_47724, biotools:tcdb | https://bio.tools/tcdb | SCR_004490 | Transporter Classification Database | 2026-08-03 09:32:40 | 311 | ||||
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NCBI BLAST Resource Report Resource Website 10000+ mentions |
NCBI BLAST (RRID:SCR_004870) | BLAST | sequence analysis software, web service, software application, data processing software, data analysis software, data access protocol, software resource | Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences. | genome, similarity, sequence, nucleotide, protein, gene, data, bio.tools |
is used by: MITE-Tracker is used by: Cello2Go is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: G-BLASTN is related to: genBlastA has parent organization: NCBI is required by: RelocaTE works with: Whole Genome Shotgun (WGS) Project works with: BLASTClust works with: MOLE-BLAST works with: Genotyping |
National Library of Medicine | PMID:16845079 PMID:18440982 |
Free, Freely available, Tutorial available | OMICS_01436, nlx_84530, biotools:blast | http://blast.ncbi.nlm.nih.gov, https://bio.tools/blast, https://sources.debian.org/src/ncbi-blast+/ | SCR_004870 | NCBI Basic Local Alignment Search Tool, NCBI BLAST, Basic Local Alignment Search Tool, BLAST | 2026-08-03 09:32:44 | 15381 | ||||
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Philius Resource Report Resource Website |
Philius (RRID:SCR_004625) | Philius | production service resource, data analysis service, analysis service resource, service resource, software resource | Web server that predicts protein transmembrane topology and signal peptides. Hidden Markov models (HMM) have been successfully applied to the tasks of transmembrane protein topology prediction and signal peptide prediction. They expand upon this work by making use of the more powerful class of dynamic Bayesian networks (DBN). Their model, Philius, is inspired by a previously published HMM, Phobius, and combines a signal peptide sub-model with a transmembrane sub-model. They introduce a two-stage DBN decoder which combines the power of posterior decoding with the grammar constraints of Viterbi-style decoding. Philius also provides protein type, segment, and topology confidence metrics to aid in the interpretation of the predictions. | hidden markov model, protein type, segment, topology, confidence metric, prediction, protein, transmembrane, signal peptide, peptide, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:18989393 | nlx_62426, biotools:philius | https://bio.tools/philius | SCR_004625 | 2026-08-03 09:32:42 | 0 | |||||||
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SMART Resource Report Resource Website 5000+ mentions |
SMART (RRID:SCR_005026) | SMART | production service resource, data analysis service, web service, service resource, database, analysis service resource, data access protocol, data or information resource, software resource | Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures. | extracellular, gene, genetic, genetically, genome, architecture, chromatin, domain, mobile, phyletic, protein, proteome, signaling, structure, taxonomic, tertiary, bio.tools, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is listed by: bio.tools is listed by: Debian is related to: Eukaryotic Linear Motif is related to: Conserved Domain Database is related to: GOTaxExplorer has parent organization: EMBL - Bork Group |
European Union | PMID:18978020 PMID:16381859 PMID:14681379 PMID:10592234 PMID:9847187 PMID:9600884 |
Free, Freely available | nif-0000-03471, biotools:smart | http://smart.embl-heidelberg.de/, https://bio.tools/smart | SCR_005026 | Simple Modular Architecture Research Tool | 2026-08-03 09:32:35 | 6760 | ||||
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MetaPhlAn Resource Report Resource Website 500+ mentions |
MetaPhlAn (RRID:SCR_004915) | sequence analysis software, software application, data processing software, data analysis software, software resource, data analysis resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. It relies on unique clade-specific marker genes identified from reference genomes. | microbial community, microbial composition, microbial genome, microbial sequence |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian has parent organization: Bitbucket has parent organization: Harvard T.H. Chan School of Public Health |
PMID:22688413 DOI:10.1038/nmeth.3589 |
OMICS_02286 | http://huttenhower.sph.harvard.edu/metaphlan https://bitbucket.org/nsegata/metaphlan/, https://sources.debian.org/src/metaphlan2/ | SCR_004915 | MetaPhlAn, Metagenomic Phylogenetic Analysis, MetaPhlAn version 2, MetaPhlAn - Metagenomic Phylogenetic Analysis, MetaPhlAn v2 | 2026-08-03 09:32:33 | 637 | |||||||
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PHAge Search Tool Resource Report Resource Website 100+ mentions |
PHAge Search Tool (RRID:SCR_005184) | PHAST | production service resource, data analysis service, data or information resource, analysis service resource, service resource, data set | A web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage cornerstone feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage quality and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. Databases available for download include Virus DB, Prophage and virus DB, Bacteria DB, and PHAST result DB. Pre-calculated genomes for viewing are also available. | prophage sequence, genome, prophage, sequence, bacterial genome, plasmid, dna sequence, graph, phage, annotate, virus, nucleotide sequence, fasta, annotated genome, genbank, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Alberta; Alberta; Canada |
PMID:21672955 | Acknowledgement requested | biotools:phast, OMICS_00180 | https://bio.tools/phast | SCR_005184 | PHAST - PHAge Search Tool | 2026-08-03 09:32:48 | 225 | |||||
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FLASH Resource Report Resource Website 1000+ mentions |
FLASH (RRID:SCR_005531) | FLASh | sequence analysis software, software application, data processing software, data analysis software, software resource | Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: shovill is related to: CLIP-Explorer has parent organization: Johns Hopkins University; Maryland; USA |
NLM R01 LM006845; NIGMS R01 GM083873; NHGRI R01 HG006677 |
PMID:21903629 | Free, Available for download, Freely available | biotools:flash, OMICS_01047 | https://sourceforge.net/projects/flashpage/files/, https://bio.tools/flash, https://sources.debian.org/src/flash/ | SCR_005531 | Fast Length Adjustment of SHort reads, Fast Length Adjustment of Short reads | 2026-08-03 09:32:52 | 2175 | ||||
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ngsTools Resource Report Resource Website 50+ mentions |
ngsTools (RRID:SCR_005489) | ngsTools | software resource, data processing software, software application, data analysis software | A collection of software programs for population genetics analyses from NGS (Next-Generation Sequencing) data, taking into account its statistical uncertainty. The methods implemented in these programs do not rely on SNP (Single Nucleotide Polymorphism) or genotype calling, and are particularly suitable for low sequencing depth data. | java, next-generation sequencing, population, genetics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24458950 | GNU General Public License, v3, Acknowledgement requested | OMICS_02248, biotools:ngstools | https://bio.tools/ngstools | SCR_005489 | 2026-08-03 09:32:42 | 53 | ||||||
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SolexaQA Resource Report Resource Website 100+ mentions |
SolexaQA (RRID:SCR_005421) | SolexaQA | sequence analysis software, software application, data processing software, data analysis software, software resource, data visualization software | Software package to calculate sequence quality statistics and create visual representations of data quality for Illumina's second-generation sequencing technology. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20875133 | Acknowledgement requested | biotools:solexaqa, OMICS_01078 | https://bio.tools/solexaqa | SCR_005421 | 2026-08-03 09:32:52 | 291 | ||||||
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Sybil Resource Report Resource Website 10+ mentions |
Sybil (RRID:SCR_005593) | Sybil | data or information resource, software resource, database | A web-based software package for comparative genomics. | comparative genomics, genome, synteny, protein cluster, protein, gene, genomic region, synteny gradient, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22121156 | OMICS_00945, biotools:sybil | https://bio.tools/sybil | SCR_005593 | Sybil: Web-based software for comparative genomics | 2026-08-03 09:32:43 | 37 | ||||||
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CLIPZ Resource Report Resource Website 10+ mentions |
CLIPZ (RRID:SCR_005755) | CLIPZ | production service resource, data analysis service, data or information resource, database, analysis service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets. | rna-binding protein, binding site, protein, functional annotation, cross-linking and immunoprecipitation, short read, mrna-seq, digital gene expression, small rna cloning, visualization, mining, analysis, post-transcriptional regulatory element, genome, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: University of Basel; Basel; Switzerland |
PMID:21087992 | THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_02256, biotools:clipz | https://bio.tools/clipz | SCR_005755 | 2026-08-03 09:32:55 | 20 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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