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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Imaging Probe Development Center (IPDC) Resource Report Resource Website |
Imaging Probe Development Center (IPDC) (RRID:SCR_006744) | IPDC | data or information resource, database | A core synthesis facility dedicated to the preparation of imaging probes, initially for intramural NIH scientists, and later, for the extramural scientific community. The IPDC provides a mechanism for the production of sensitive probes for use by imaging scientists who cannot obtain such probes commercially. The probes to be made will encompass all major imaging modalities including radionuclide, magnetic resonance, and optical. Nearly all of these imaging probes are not commercially available, nor are they viable commercial products, and most are new compositions-of-matter (http://nihlibrary.ors.nih.gov/ipdcdb/IPDCDB_Search.asp). The IPDC was born from the realization that imaging technologies will be crucial in basic, translational, and clinical research in the 21st century, and that the synthetic chemistry required to reliably produce imaging probes lies at the heart of research within imaging technologies. To this end, the IPDC has recruited the equipment and expertise to concurrently synthesize multiple types of imaging probes for bioscientists with diverse research interests, encompassing all imaging modalities, including optical, radionuclide, ultrasound, and magnetic resonance. The IPDC embodies an exciting new approach to apply and combine chemistry and imaging sciences toward specific problems in biology and medical sciences, and will be a truly interdisciplinary effort aimed at maximizing returns from the revolutionary new discoveries being described in modern imaging. A significant part of the IPDC will also be directed, independently, to the discovery of new imaging approaches and compositions. The IPDC houses scientific staff, mostly chemists, who have interests and expertise in one or more aspects of molecular imaging. The IPDC is generating known and novel imaging probes for targeting receptors, cells, and tissues, and for preclinical in vivo evaluations by its intramural collaborators. Many such interesting agents have been described in the scientific literature, but are often not explored further due to lack of a reliable supply of reagent. One aspect of the IPDC''s mission is to rectify this situation. IPDC-supplied reagents will not be limited to one imaging modality, but will include the flexible application of diverse technologies. Also, the IPDC will seek to develop novel state-of-the-art imaging probes in collaboration with biological and biomedical intramural scientists who can provide or suggest suitable targeting agent/receptor pairs. The Imaging Probe Development Center (IPDC) was initiated in the incubator space of the Common Fund and has transitioned to the intramural program of the National Heart, Lung, and Blood Institute. | imaging, probe, optical, radionuclide, ultrasound, magnetic resonance, ct, x-ray, fmri, mri, near ir fluorescence, pet, spect, tem, molecular library | has parent organization: NHLBI Division of Intramural Research | NIH Roadmap for Medical Research | PMID:17994866 | nlx_146256 | SCR_006744 | Imaging Probe Development Center | 2026-08-29 11:29:48 | 0 | ||||||
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CAPS Database Resource Report Resource Website 1+ mentions |
CAPS Database (RRID:SCR_006862) | CAPS-DB | data or information resource, database | It is a structural classification of helix-cappings or caps compiled from protein structures. Caps extracted from protein structures have been structurally classified based on geometry and conformation and organized in a tree-like hierarchical classification where the different levels correspond to different properties of the caps. CASP-DB is fully browsable and searchable and is regularly updated. The regions of the polypeptide chain immediately preceding or following a helix are known as Nt- and Ct cappings, respectively. Cappings play a central role stabilizing helices due to lack of intrahelical hydrogen bonds in the first and last turn. Sequence patterns of amino acid type preferences have been derived for cappings but the structural motifs associated to them are still unclassified. CAPS-DB is a database of clusters of structural patterns of different capping types. The clustering algorithm is based in the geometry and the space conformation of these regions. CAPS-DB is a relational database that allows the user to search, browse, inspect and retrieve structural data associated to cappings. The contents of CAPS-DB might be of interest to a wide range of scientist covering different areas such as protein design and engineering, structural biology and bioinformatics. CapsDB v4.0 * PDB structures: 4591 * Number of clusters: 859 * Number of caps: 31452 | structural classification, helix-capping, protein engineering, clustering, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Aberystwyth University; Wales; United Kingdom |
Research Councils United Kingdom Academic Fellow scheme ; Leeds Institute of Molecular Medicine ; MICINN and FEDER BIO2011-22568 |
PMID:22021380 | biotools:caps-db, nlx_149414 | http://www.bioinsilico.org/CAPSDB, https://bio.tools/caps-db | SCR_006862 | CAPS - Database | 2026-08-29 11:29:53 | 2 | |||||
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SCOP: Structural Classification of Proteins Resource Report Resource Website 50+ mentions |
SCOP: Structural Classification of Proteins (RRID:SCR_007039) | data or information resource, database | The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. Protein domains in SCOP are hierarchically classified into families, superfamilies, folds and classes. The continual accumulation of sequence and structural data allows more rigorous analysis and provides important information for understanding the protein world and its evolutionary repertoire. SCOP participates in a project that aims to rationalize and integrate the data on proteins held in several sequence and structure databases. As part of this project, starting with release 1.63, we have initiated a refinement of the SCOP classification, which introduces a number of changes mostly at the levels below superfamily. The pending SCOP reclassification will be carried out gradually through a number of future releases. In addition to the expanded set of static links to external resources, available at the level of domain entries, we have started modernization of the interface capabilities of SCOP allowing more dynamic links with other databases. | bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: IndelFR - Indel Flanking Region Database is related to: SUPFAM is related to: DOMMINO - Database Of MacroMolecular INteractiOns has parent organization: MRC Laboratory of Molecular Biology |
PMID:14681400 | nlx_94704, biotools:scop | https://bio.tools/scop | SCR_007039 | Structural Classification of Proteins database, SCOP database | 2026-08-29 11:29:55 | 98 | |||||||
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Protein Ligand Database Resource Report Resource Website |
Protein Ligand Database (RRID:SCR_006980) | PLD | data or information resource, database | It is a publicly available web-based database that aims to provide further understanding of protein-ligand interactions. It''s a resource containing biomolecular data, including binding energies, Tanimoto ligand similarity scores and protein sequence similarities of protein-ligand complexes. The PLD contains biomolecular data including calculated binding energies, Tanimoto ligand similarity scores and protein percentage sequence similarities. The database has potential for application as a tool in molecular design. | binding energy, biomolecular, interaction, ligand, protein, protein sequence | nif-0000-20902 | http://www-mitchell.ch.cam.ac.uk/pld/ | SCR_006980 | Protein Ligand Database | 2026-08-29 11:29:49 | 0 | ||||||||
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Gait Dynamics in Neuro-Degenerative Disease Data Base Resource Report Resource Website 1+ mentions |
Gait Dynamics in Neuro-Degenerative Disease Data Base (RRID:SCR_006979) | data or information resource, database | Database of records from patients with Parkinson's disease (n = 15), Huntington's disease (n = 20), or amyotrophic lateral sclerosis (n = 13). Records from 16 healthy control subjects are also included here. The raw data were obtained using force-sensitive resistors, with the output roughly proportional to the force under the foot. Stride-to-stride measures of footfall contact times were derived from these signals. | gait, neurodegenerative disease, database, parkinson, huntington, als |
is used by: NIF Data Federation has parent organization: Physiobank |
Parkinson's disease, Huntington's disease, Amyotrophic Lateral Sclerosis | Acknowledgement requested | nlx_64373 | SCR_006979 | Gait Dynamics in Neurodegenerative Disease, Gait Dynamics in Neuro-Degenerative Disease DataBase, Gait Dynamics in Neuro-Degenerative Disease Data Base | 2026-08-29 11:29:46 | 3 | |||||||
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Dali database Resource Report Resource Website 1+ mentions |
Dali database (RRID:SCR_006974) | data or information resource, database | Resource out of service. Documented on May, 5th, 2021.The Dali Database is based on all-against-all 3D structure comparison of protein structures in the Protein Data Bank (PDB). The structural neighborhoods and alignments are automatically maintained and regularly updated using the Dali search engine. The Dali Database contains structural alignments of PDB90 versus the full PDB using DaliLite. The data can be viewed interactively here, or downloaded in its entirety Users may search by PDB identifier or keyword. | protein, protein 3d structure, protein structure | has parent organization: University of Helsinki; Helsinki; Finland | PMID:20457744 | nif-0000-02719 | SCR_006974 | Dali Database | 2026-08-29 11:29:54 | 4 | ||||||||
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NeuroSNP Project Resource Report Resource Website 1+ mentions |
NeuroSNP Project (RRID:SCR_007029) | NeuroSNP | data or information resource, database | The goal of this project is to aid genetic association studies of addiction by creating a resource of biologically relevant genes, pathways and single nucleotide polymorphisms (SNPs). The primary users of the NeuroSNP resource are investigators conducting genome-wide association studies (GWASs) of addiction-related phenotypes. NeuroSNP will allow investigators to identify biologically relevant genes for addiction based on curated expert knowledge, and assess the coverage of these genes provided by commercial SNP microarrays. If investigators wish to ensure the coverage of certain addiction-related genes is optimal, NeuroSNP provides a mechanism for supplementation. While commercial SNP microarrays offer affordable and comprehensive coverage of the human genome, some diseases have biologically relevant genomic regions that may require additional coverage. Addiction, for example, is believed to be influenced by complex interactions involving several genes and pathways. NIDA has assembled a number of investigators specializing in fields such as genetics, pharmacogenetics, bioinformatics and neurobiology through a Request for Information. These investigators have pooled their expert knowledge to produce a database of addiction-related genes and SNPs. Commercial SNP microarrays, such as those offered by Affymetrix and Illumina, are then analyzed to determine how well certain addiction-related genes are covered. When the coverage is less than optimal, a SNP prioritization scheme is used to supplement the commercial array with the most biologically informative markers. For example, SNPs in coding regions, promoters, and evolutionary conserved regions are selected first. | has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA | nif-0000-21983 | SCR_007029 | NeuroSNP Project | 2026-08-29 11:29:47 | 3 | |||||||||
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Bipolar Disorder Neuroimaging Database Resource Report Resource Website 1+ mentions |
Bipolar Disorder Neuroimaging Database (RRID:SCR_007025) | BiND | data or information resource, database | Database of 141 studies which have investigated brain structure (using MRI and CT scans) in patients with bipolar disorder compared to a control group. Ninety-eight studies and 47 brain structures are included in the meta-analysis. The database and meta-analysis are contained in an Excel spreadsheet file which may be freely downloaded from this website. | magnetic resonance imaging assay, cat imaging assay, mri, brain, neuroimaging, normal control, image | has parent organization: King's College London; London; United Kingdom | Bipolar Disorder | King's College London; England; United Kingdom ; National Institute for Health Research NIHR Biomedical Research Centre for Mental Health ; South London and Maudsley NHS Foundation ; MRC |
PMID:18762588 | nlx_149352 | SCR_007025 | Bipolar Disorder Neuroimaging Database (BiND) | 2026-08-29 11:29:49 | 3 | |||||
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Database of Chemical Compounds and Reactions in Biological Pathways Resource Report Resource Website 1+ mentions |
Database of Chemical Compounds and Reactions in Biological Pathways (RRID:SCR_006851) | data or information resource, database | KEGG LIGAND contains knowledge of chemical substances and reactions that are relevant to life. It is a composite database consisting of COMPOUND, GLYCAN, REACTION, RPAIR, and ENZYME databases, whose entries are identified by C, G, R, RP, and EC numbers, respectively. ENZYME is derived from the IUBMB/IUPAC Enzyme Nomenclature, but the others are internally developed and maintained. The primary database of KEGG LIGAND is a relational database with the KegDraw interface, which is used to generated the secondary (flat file) database for DBGET. | enzyme, chemical substance, compound, glycan, life, reaction, software | is listed by: 3DVC | nif-0000-20832 | SCR_006851 | LIGAND | 2026-08-29 11:29:48 | 2 | |||||||||
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RAP-DB Resource Report Resource Website 500+ mentions |
RAP-DB (RRID:SCR_006610) | RAP-DB | data or information resource, database | Database that provides the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. RAP-DB contains clone positions, structures and functions of genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. | genome sequence assembly, International Rice Genome Sequencing Project, manually curated annotation, sequence, genomics information, |
has parent organization: National Institute of Genetics; Shizuoka; Japan has parent organization: National Institute of Agrobiological Sciences; Ibaraki; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT NT05-3 42996 | PMID:23299411 PMID:18089549 |
Free, Freely available | SCR_015062, nif-0000-03385 | http://rapdb.lab.nig.ac.jp/ | SCR_006610 | Rice Annotation Project, Rice Annotation Project Database | 2026-08-29 11:29:51 | 837 | ||||
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Consensus CDS Resource Report Resource Website 100+ mentions |
Consensus CDS (RRID:SCR_006729) | CCDS | data or information resource, database | Database (anonymous FTP) resulting from a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality. The long term goal is to support convergence towards a standard set of gene annotations. Collaborators are EBI, NCBI, UCSC, WTSI and the initial results are also available from the participants'''' genome browser Web sites. In addition, CCDS identifiers are indicated on the relevant NCBI RefSeq and Entrez Gene records and in Map Viewer displays of RNA (RefSeq) and Gene annotations on the reference assembly. | human genome sequence, human protein, mouse genome sequence, mouse protein, protein coding region, gene, genome sequence, genome, sequence, gene annotation, protein, gold standard |
is listed by: OMICtools is related to: Entrez Gene is related to: HomoloGene is related to: MapViewer is related to: VEGA has parent organization: NCBI has parent organization: European Bioinformatics Institute has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom has parent organization: University of California at Santa Cruz; California; USA |
PMID:24217909 PMID:22434842 PMID:19498102 |
The community can contribute to this resource, Acknowledgement requested | nif-0000-02645, OMICS_01535 | http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi | SCR_006729 | CCDS Database, NCBI Consensus CDS protein set, NCBI CCDS Database | 2026-08-29 11:29:52 | 242 | |||||
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GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool Resource Report Resource Website 500+ mentions |
GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool (RRID:SCR_006848) | GOrilla | analysis service resource, data analysis service, production service resource, service resource | A tool for identifying and visualizing enriched GO terms in ranked lists of genes. It can be run in one of two modes: * Searching for enriched GO terms that appear densely at the top of a ranked list of genes or * Searching for enriched GO terms in a target list of genes compared to a background list of genes. | gene, genetic, ontology, ontology or annotation visualization, statistical analysis, term enrichment, visualization, analysis, protein |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology |
European Union FP6 ; Yeshaya Horowitz Association |
PMID:19192299 | Acknowledgement requested, Free, Public | nlx_80425, OMICS_02282 | SCR_006848 | Gene Ontology enRIchment anaLysis and visuaLizAtion tool, GOrilla: Gene Ontology Enrichment Analysis Visualization Tool | 2026-08-29 11:29:45 | 524 | |||||
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TM Function Database Resource Report Resource Website 1+ mentions |
TM Function Database (RRID:SCR_007058) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Database of functional residues in alpha-helical and beta-barrel membrane proteins. Each protein is identified with its name and source alongwith the Uniprot code. The protein data bank (PDB) codes are also given for available proteins. Different methods and experimental parameters, for example, affinity, dissociation constant, IC50, activity etc. are given in the database. Further, the database provides the numerical experimental value for each residue (or mutant) in a protein. The experimental data are collected from the literature both by searching the journals as well as with the keyword search at PUBMED. In addition, complete reference is given with journal citation and PMID number. TNFunction is cross-linked with the sequence database, Uniprot, structural database, PDB, and literature database, PubMed. The WWW interface enables users to search data based on various terms with different display options for outputs. | functional residue, active sites, binding affinity, dissociation constant, membrane protein, protein data bank, protein sequence database, protein sequence motif, protein uniprot, sequence structure function relationship of membrane proteins, maximal velocity of transport | has parent organization: National Institute of Advanced Industrial Science and Technology | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-08632, nif-0000-06665, SCR_007057 | SCR_007058 | TMFunction Database | 2026-08-29 11:29:47 | 1 | ||||||||
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SysZNF - C2H2 Zinc Finger genes Resource Report Resource Website |
SysZNF - C2H2 Zinc Finger genes (RRID:SCR_007056) | SysZNF | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 2, 2016. SysZNF is an information resource for C2H2 Zinc Finger genes in humans and mice. C2H2 Zinc Finger genes (C2H2-ZNF) constitute the largest class of transcription factors in humans and mouse. C2H2 zinc finger proteins primarily bind to DNA. In most cases, they attach to regions near certain genes and turn the genes on and off as needed. The researches on these genes show light on the evolution of gene regulation systems and development. Therefore, we develop SysZNF (Systematical information resource of Zinc Finger genes) to collect the information related to C2H2 Zinc Finger genes. The aim of SysZNF was to provide a user-friendly interface for rendering the information (DNA, Expression, Protein, Reference and so on) of each C2H2-ZNF (e.g., ZNF10) and to enable a comprehensive analysis of C2H2-ZNF. This project was supported by the Proteome-Center at Rostock University (PCRU) who conceives the concept of the database and Key laboratory of Systems biology at the Shanghai Institute for Biological Sciences (SIBS) who implemented the database. It is maintained jointly by PCRU and SIBS. | zinc finger protein, zinc finger, cysteine, histidine, zinc ion, gene |
has parent organization: University of Rostock; Mecklenburg-Vorpommern; Germany has parent organization: Chinese Academy of Sciences; Beijing; China |
BMBF 2007DFA31040; Chinese Academy of Sciences CHN07/38 |
PMID:18974185 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03530 | SCR_007056 | SysZNF: the C2H2 Zinc Finger Gene Database, SysZNF: the Zinc Finger gene database | 2026-08-29 11:29:55 | 0 | |||||
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HIV-1 Human Protein Interaction Database Resource Report Resource Website 10+ mentions |
HIV-1 Human Protein Interaction Database (RRID:SCR_006879) | HIV-1 Human Protein Interaction Database | data or information resource, database | A database of interactions between HIV-1 and human proteins published in the peer-reviewed literature. The goal is to provide a concise, yet detailed, summary of all known interactions of HIV-1 proteins with host cell proteins, other HIV-1 proteins, or proteins from disease organisms associated with HIV/AIDS. For each HIV-1 human protein interaction the following information is provided: * NCBI Reference Sequence (RefSeq) protein accession numbers. * NCBI Entrez Gene ID numbers. * Amino acids from each protein that are known to be involved in the interaction. * Brief description of the protein-protein interaction. * Keywords to support searching for interactions. * PubMed identification numbers (PMIDs) for all journal articles describing the interaction. In addition, all protein-protein interactions documented in the database are integrated into Entrez Gene records and listed in the ''HIV-1 protein interactions'' section of Entrez Gene reports. The database is also tightly linked to other databases through Entrez Gene, enabling users to search for an abundance of information related to HIV pathogenesis and replication. | protein-protein interaction, protein, interaction, cellular protein |
is related to: VirHostNet: Virus-Host Network has parent organization: NCBI |
Human immunodeficiency virus, Type 1 | NIAID contract N01-AI-05415; NIAID N01-AI-70042 |
PMID:18927109 PMID:19025396 PMID:19262354 |
Acknowledgement requested | nif-0000-02964 | SCR_006879 | HIV-1: Human Protein Interaction Database, Human immunodeficiency virus type 1 human protein interaction database at NCBI | 2026-08-29 11:29:45 | 13 | ||||
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The Loom Resource Report Resource Website 1+ mentions |
The Loom (RRID:SCR_006877) | Loom | blog, data or information resource, narrative resource | The Loom is a blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer. Carl Zimmer writes about science regularly for the New York Times and magazines such as Discover, where he is a contributing editor and columnist. | has parent organization: Discover Magazine | nlx_83062 | SCR_006877 | 2026-08-29 11:29:53 | 1 | ||||||||||
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MyHits Resource Report Resource Website 10+ mentions |
MyHits (RRID:SCR_006757) | data or information resource, database | Database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them. | protein, domain, motif, sequence, predictor, markov, model, gene, expression, mysql, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:17545200 | Free | nif-0000-02962, biotools:myhits | https://bio.tools/myhits | SCR_006757 | MyHit | 2026-08-29 11:29:44 | 41 | ||||||
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Sapienta Resource Report Resource Website 1+ mentions |
Sapienta (RRID:SCR_006993) | SAPIENTA | software application, software resource, source code | Software to help researchers process scientific papers faster and get the information they are interested in out of them. This is achieved by automating the recognition of core scientific concepts such as Motivation, Method, Result, Conclusion in papers and uses them to generate automatic summaries. This SAPIENTA tool adds additional functionality to the SAPIENT tool, an annotation tool implemented as a web application which enables experts to annotate scientific papers, sentence by sentence manually, according to the Core Scientific Concept (CSC) schema. | semantic mark up, semantic, annotation, annotation software | is listed by: FORCE11 | JISC | nlx_151311 | SCR_006993 | SAPIENTA - Automating the Semantic Annotation of Papers, Semantic Annotation of Papers: Interface & ENrichment Tool Automated | 2026-08-29 11:29:47 | 1 | |||||||
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Amino Acid Index Database Resource Report Resource Website 100+ mentions |
Amino Acid Index Database (RRID:SCR_007044) | data or information resource, database | AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. AAindex consists of three sections now: AAindex1 for the amino acid index of 20 numerical values, AAindex2 for the amino acid mutation matrix and AAindex3 for the statistical protein contact potentials. All data are derived from published literature. An amino acid index is a set of 20 numerical values representing any of the different physicochemical and biological properties of amino acids. The AAindex1 section of the Amino Acid Index Database is a collection of published indices together with the result of cluster analysis using the correlation coefficient as the distance between two indices. This section currently contains 544 indices. Another important feature of amino acids that can be represented numerically is the similarity between amino acids. Thus, a similarity matrix, also called a mutation matrix, is a set of 210 numerical values, 20 diagonal and 20x19/2 off-diagonal elements, used for sequence alignments and similarity searches. The AAindex2 section of the Amino Acid Index Database is a collection of published amino acid mutation matrices together with the result of cluster analysis. This section currently contains 94 matrices. In the release 9.0, we added a collection of published protein pairwise contact potentials to AAindex as AAindex3. This section currently contains 47 contact potential matrices. Sponsors: This work was supported by grants and resources from the Ministry of Education, Culture, Sports, Science and Technology, and the Japan Science and Technology Agency, and the Bioinformatics Center, Institute for Chemical Research, Kyoto University and the Super Computer System, Human Genome Center, Institute of Medical Science, University of Tokyo. | amino acid, biochemical property, mutation, physicochemical property, protein sequence, proteomics, FASEB list | has parent organization: GenomeNet | PMID:3244698 PMID:9053899 PMID:9847231 PMID:10592278 |
nif-0000-02527 | SCR_007044 | AAindex | 2026-08-29 11:29:47 | 218 | ||||||||
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UniTrap Resource Report Resource Website 1+ mentions |
UniTrap (RRID:SCR_007046) | data or information resource, database | A curated collection of all the trapped ES cell clones. Gene-trapping is a valuable tool that uses random mutagenesis to create hypomorphic or null alleles by insertion of exogenous DNA. Since numerous public and private projects have been performing gene trapping over the last few years,it is natural that large overlaps exist and some vectors produce better knock-outs than others due to their insertion site. Considering the high need to develop a comprehensive database that would include both public and private data to provide public access to this essential biological resource, we developed UniTrap, a curated collection of all the trapped ES cell clones, collected from public and private databases. We have developed a bioinformatics pipeline to automate the identification and characterization of trapped genes starting from their transcriptional sequence tags.We process gene trap sequence tags from ES cell clones to generate ‘UniTraps’, i.e. distinct collections of unambiguous insertions at the same subgenic region of annotated genes (RefSeq and Ensembl genes). The UniTrap resource contains data relative to well-known trapped genes. We aim to provide the wet lab researchers with a comprehensive, regularly updated database and curated tools for(i) identifying and comparing the clones carrying a trap into the genes of interest,(ii) evaluating the severity of the mutation to the protein function in each independent trapping event, and(iii) supplying complete information to perform PCR, RT-PCR and restriction experiments to verify the clone and identify the exact point of vector insertion. | es cell clones, gene-trapping, pcr, rt-pcr | nif-0000-03615 | SCR_007046 | UniTrap | 2026-08-29 11:29:55 | 3 |
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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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