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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Sequence Tag Alignment and Consensus Knowledgebase Database Resource Report Resource Website |
Sequence Tag Alignment and Consensus Knowledgebase Database (RRID:SCR_002156) | data or information resource, data processing software, data visualization software, database, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The STACKdb is knowledgebase generated by processing EST and mRNA sequences obtained from GenBank through a pipeline consisting of masking, clustering, alignment and variation analysis steps. The STACK project aims to generate a comprehensive representation of the sequence of each of the expressed genes in the human genome by extensive processing of gene fragments to make accurate alignments, highlight diversity and provide a carefully joined set of consensus sequences for each gene. The STACK project is comprised of the STACKdb human gene index, a database of virtual human transcripts, as well as stackPACK, the tools used to create the database. STACKdb is organized into 15 tissue-based categories and one disease category. STACK is a tool for detection and visualization of expressed transcript variation in the context of developmental and pathological states. The data system organizes and reconstructs human transcripts from available public data in the context of expression state. The expression state of a transcript can include developmental state, pathological association, site of expression and isoform of expressed transcript. STACK consensus transcripts are reconstructed from clusters that capture and reflect the growing evidence of transcript diversity. The comprehensive capture of transcript variants is achieved by the use of a novel clustering approach that is tolerant of sub-sequence diversity and does not rely on pairwise alignment. This is in contrast with other gene indexing projects. STACK is generated at least four times a year and represents the exhaustive processing of all publicly available human EST data extracted from GenBank. This processed information can be explored through 15 tissue-specific categories, a disease-related category and a whole-body index | exonic, expressed, expressed sequence tag (est), expression, fragment, gene, alignment, alternative gene, cdna, clone, cluster, developmental, disease, diversity, genome, homo sapiens, human, isoform, knowledgebase, meta-cluster, mrna, pathological, sequence, tissue, transcript, variant, visualization | PMID:11125101 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20946 | SCR_002156 | STACKdb | 2026-09-12 01:00:07 | 0 | ||||||||
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Neal's DNA Mutation Site Resource Report Resource Website 1+ mentions |
Neal's DNA Mutation Site (RRID:SCR_002947) | Neal's DNA Mutation Site | data analysis software, data or information resource, data processing software, database, portal, software application, software resource, topical portal | This site provides access to mutation databases and software including the human hprt database, Human p53 database, Transgenic lacZ database, and Transgenic lacI database. Other avaialble programs include Mutational spectra comparison and relational database data entry. The most recent hprt database contains information on over 2,300 mutations found in vivo and in vitro in the human hprt gene and runs under Windows. The version for evaluation on this homepage has fewer mutations and is a DOS program. The database contains information on the mutagen, dose, spontaneous and induced mutant fraction, base position, amino acid position, amino acid change, local DNA sequence, cell type, citation, and other items. In addition, information regarding the cause and effect of mutations affecting splicing is given. Routines have been developed for the analysis of single base substitutions. The p53 database contains information on nearly 5,867 mutations found in the human p53 gene. The database itself has been updated in April of 1997. The database contains information on the cancer type, loss of heterozygosity, base position, amino acid position, amino acid change, local DNA sequence,citation, and other items. Routines have been developed for the analysis of single base substitutions. The Transgenic lacZ database contains information on 405 mutations found in vivo in the transgenic lacZ gene. It has last been updated in January of 1998. It provides information on the mutagen, dose, organ, mutant fraction, base position, amino acid position, amino acid change, local DNA sequence, citation, and other items. The Transgenic lacI database contains information on over 1700 mutations found in vivo in the transgenic lacI gene and on nearly 8000 mutations in the lacI gene in native E. coli. The database was updated in January 1998. The database contains information on the mutagen, dose, organ, mutant fraction, base position, amino acid position, amino acid change, local DNA sequence, citation, and other items. Routines have been developed for the analysis of single base substitutions for each of the databases. The software runs only on IBM-compatible PCs. | human, mouse | has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA | Free, Available for download, Freely available | nif-0000-02995 | SCR_002947 | Human p53 Human hprt Rodent lacI and Rodent lacZ Databases and Software, Human p53 Human hprt Rodent lacI and Rodent lacZ Databases, Human p53 Human hprt Rodent lacI Rodent lacZ Databases | 2026-09-12 01:00:09 | 4 | |||||||
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Pathway Analysis Tool for Integration and Knowledge Acquisition Resource Report Resource Website 1+ mentions |
Pathway Analysis Tool for Integration and Knowledge Acquisition (RRID:SCR_002100) | PATIKA | data or information resource, database, pathway analysis software | The human pathway database which contains different biological entities and reactions and software tools for analysis. PATIKA Database integrates data from several sources, including Entrez Gene, UniProt, PubChem, GO, IntAct, HPRD, and Reactome. Users can query and access this data using the PATIKAweb query interface. Users can also save their results in XML or export to common picture formats. The BioPAX and SBML exporters can be used as part of this Web service. | human, pathway, reaction, database, pathway analysis software, web service, biological entity, biological reaction |
uses: Entrez Gene uses: UniProt uses: PubChem uses: Gene Ontology uses: IntAct uses: HPRD - Human Protein Reference Database uses: Reactome |
PMID:12117798 PMID:14960461 |
THIS RESOURCE IS NO LONGER IS SERVICE. | nif-0000-20882 | http://www.cs.bilkent.edu.tr/~patikaweb/ | SCR_002100 | Pathway Analysis Tool for Integration and Knowledge Acquisition (PATIKA), PATIKA - Pathway Analysis Tools for Integration and Knowledge Acquisition | 2026-09-12 01:00:07 | 2 | |||||
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University of California at Los Angeles, School of Medicine: Neuro Imaging Lab of Thompson Resource Report Resource Website |
University of California at Los Angeles, School of Medicine: Neuro Imaging Lab of Thompson (RRID:SCR_001924) | curriculum material, data or information resource, narrative resource, slide, training material, video resource | The UCLA laboratory of neuroimaging is working in several areas to enhance knowledge of anatomy, including brain mapping in large human populations, HIV, Schizophrenia, methamphetamine, tumor growth and 4d brain mapping, genetics and detection of abnormalities. | engineer, genetics, abnormality, alzheimer's, anatomy, atlas, brain, computational, cortical, dementia, disease, growth, histologic, hiv, human, image, knowledge, mapping, mathematical, mathematician, medical doctor, methamphetamine, model, mri, neuroscientist, pet, polymorphism, population, schizophrenia, spect, structure, tumor, neuroimaging | has parent organization: University of California at Los Angeles; California; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10496 | SCR_001924 | UCLA, Thompson Lab | 2026-09-12 01:00:07 | 0 | ||||||||
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ConnectomeDB Resource Report Resource Website 50+ mentions |
ConnectomeDB (RRID:SCR_004830) | ConnectomeDB | data or information resource, data repository, database, image collection, image repository, service resource, storage service resource | Data management platform that houses all data generated by the Human Connectome Project - image data, clinical evaluations, behavioral data and more. ConnectomeDB stores raw image data, as well as results of analysis and processing pipelines. Using the ConnectomeDB infrastructure, research centers will be also able to manage Connectome-like projects, including data upload and entry, quality control, processing pipelines, and data distribution. ConnectomeDB is designed to be a data-mining tool, that allows users to generate and test hypotheses based on groups of subjects. Using the ConnectomeDB interface, users can easily search, browse and filter large amounts of subject data, and download necessary files for many kinds of analysis. ConnectomeDB is designed to work seamlessly with Connectome Workbench, an interactive, multidimensional visualization platform designed specifically for handling connectivity data. De-identified data within ConnectomeDB is publicly accessible. Access to additional data may be available to qualified research investigators. ConnectomeDB is being hosted on a BlueArc storage platform housed at Washington University through the year 2020. This data platform is based on XNAT, an open-source image informatics software toolkit developed by the NRG at Washington University. ConnectomeDB itself is fully open source. | brain, connectivity, human, adult human, evaluation, clinical, behavior, data set, diffusion imaging, resting-state fmri, task-evoked fmri, t1-weighted mri, t2-weighted mri, structural mapping, myelin mapping, magnetoencephalography, electroencephalography, fmri, twin |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: XNAT - The Extensible Neuroimaging Archive Toolkit has parent organization: Washington University in St. Louis; Missouri; USA works with: Connectome Workbench |
Healthy, Twin, Non-twin sibling | NIH Blueprint for Neuroscience Research ; Washington University in St. Louis; Missouri; USA ; McDonnell Center for Systems Neuroscience ; NIMH 1U54MH091657 |
PMID:22366334 | Account required, Open unspecified license, Acknowledgement required, See Data Use Terms, The community can contribute to this resource | nlx_143923 | SCR_004830 | 2026-09-12 01:00:10 | 63 | |||||
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Institute for Laboratory Animal Research Resource Report Resource Website 50+ mentions |
Institute for Laboratory Animal Research (RRID:SCR_006872) | data or information resource, narrative resource, standard specification | The mission of ILAR is to evaluate and disseminate information on issues related to the scientific, technological, and ethical use of animals and related biological resources in research, testing, and education. Using the principles of refinement, reduction, and replacement (3Rs) as a foundation, ILAR promotes high-quality science through the humane care and use of animals and the implementation of alternatives. Through the reports of expert committees, the ILAR Journal, web-based resources, and other means of communication, ILAR functions as a component of the National Academies to provide independent, objective advice to the federal government, the international biomedical research community, and the public. ILAR supports the responsible use of animals in research, testing, and education as a key component to advancing the health and quality of life of humans and animals. It promotes high-quality science and humane care and use of research animals based upon the principles of refinement, replacement, and reduction (the 3Rs) and high ethical standards. It fosters best practices that enhance human and animal welfare by organizing and disseminating information and by facilitating dialogue among interested parties. It has developed a unique Search Engine to search for animal models and strains. This search engine surveys all the websites of vendors and repositories of laboratory animals and biological material on our Links page. The ILAR develops guidelines on laboratory animal care and use and conducts conferences, symposia, and workshops on important laboratory animal problems. ILAR publishes the ILAR Journal on a quarterly basis, as well as conference proceedings and special reports prepared by committees of experts. A list of ILAR publications on issues related to laboratory animal research is available on the Web site. As part of the Animal Models and Genetic Stocks Information Exchange Program, ILAR staff members answer direct telephone and mail inquiries and maintain a Web page containing a database on animal models and genetic stock. The Web site also offers a comprehensive search engine that enables users to find information on the existence and location of special animal models, correct nomenclature to identify animals, and related topics such as diseases of animals and relevant publications. Sponsors: ILAR receives funding from the following sponsors: -Abbott Laboratories -Abbott Fund -American College of Laboratory Animal Medicine (ACLAM) -American Society of Laboratory Animal Practitioners (ASLAP) -Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC) -Bristol-Myers Squibb Co. -Charles River -Charles River Laboratories Foundation -Covance -Federation of American Societies for Experimental Biology (FASEB) -GlaxoSmithKline -Merck & Co., Inc. -National Science Foundation (NSF) -Pfizer -Scientists Center for Animal Welfare (SCAW) -U.S. Department of Agriculture (USDA) -U.S. Department of the Army -U.S. Department of Health and Human Services (DHHS) :*National Institutes of Health (NIH) :*Office of Research Integrity (ORI) -U.S. Department of the Navy -U.S. Department of Veterans Affairs -Wellcome Trust -Wyeth Pharmaceuticals | education, ethical, animal, biological, biomedical, health, human, laboratory, life, quality, research, scientific, technological, test | nif-0000-24355 | SCR_006872 | ILAR | 2026-09-12 01:00:12 | 55 | ||||||||||
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NIMH Multimedia Resource Report Resource Website |
NIMH Multimedia (RRID:SCR_005467) | data or information resource, narrative resource, podcast, video resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Audio and video available from the National Institute of Mental Health (NIMH). | human, mental health, audio, video, multimedia, podcast | has parent organization: National Institute of Mental Health | National Institute of Mental Health | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_146219 | SCR_005467 | National Institute of Mental Health Multimedia | 2026-09-12 01:00:11 | 0 | |||||||
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Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology Resource Report Resource Website 1000+ mentions |
Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology (RRID:SCR_008017) | data acquisition software, data or information resource, data processing software, database, software application, software resource | Harvester is a Web-based tool that bulk-collects bioinformatic data on human proteins from various databases and prediction servers. It is a meta search engine for gene and protein information. It searches 16 major databases and prediction servers and combines the results on pregenerated HTML pages. In this way Harvester can provide comprehensive gene-protein information from different servers in a convenient and fast manner. As full text meta search engine, similar to Google trade mark, Harvester allows screening of the whole genome proteome for current protein functions and predictions in a few seconds. With Harvester it is now possible to compare and check the quality of different database entries and prediction algorithms on a single page. Sponsors: This work has been supported by the BMBF with grants 01GR0101 and 01KW0013. | function, gene, bioinformatics, data, database, human, meta search engine, prediction, protein, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Karlsruhe Institute of Technology; Karlsruhe; Germany |
biotools:harvester, nif-0000-10169 | https://bio.tools/harvester | SCR_008017 | Harvester IV | 2026-09-12 01:00:13 | 1480 | ||||||||
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Is the Brain (Like) a Computer Resource Report Resource Website |
Is the Brain (Like) a Computer (RRID:SCR_008809) | Is the Brain (Like) a Computer | book, data or information resource, narrative resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Is the Brain (Like) a Computer is an e-book written by Prof. Mark Dubin. It consists of the following: Introduction. Why do we consider the relationship of brains and computers and what does this have to do with consciousness? What's a Brain Made Of? A thought experiment. Test Drive a Turing Machine. A theoretical approach. Interim Summary. Many of the main pages have links to additional information. When you click on one of those links a NEW page will open ON TOP of the page you are clicking from. This convention is adopted so that you can look at the additional information and then easily return to the main page you got there from. | brain, human, image | has parent organization: University of Colorado; Colorado; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144392 | SCR_008809 | Is the Brain Like a Computer?, Is the Brain Like a Computer | 2026-09-12 01:00:14 | 0 | |||||||
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Genetic and Rare Diseases Information Center Resource Report Resource Website 10+ mentions |
Genetic and Rare Diseases Information Center (RRID:SCR_008695) | GARD | data or information resource, disease-related portal, portal, topical portal | Genetic and Rare Diseases Information Center (GARD) is a collaborative effort of two agencies of the National Institutes of Health, The Office of Rare Diseases Research (ORDR) and the National Human Genome Research Institute (NHGRI) to help people find useful information about genetic conditions and rare diseases. GARD provides timely access to experienced information specialists who can furnish current and accurate information about genetic and rare diseases. So far, GARD has responded to 27,635 inquiries on about 7,147 rare and genetic diseases. Requests come not only from patients and their families, but also from physicians, nurses and other health-care professionals. GARD also has proved useful to genetic counselors, occupational and physical therapists, social workers, and teachers who work with people with a genetic or rare disease. Even scientists who are studying a genetic or rare disease and who need information for their research have contacted GARD, as have people who are taking part in a clinical study. Community leaders looking to help people find resources for those with genetic or rare diseases and advocacy groups who want up-to-date disease information for their members have contacted GARD. And members of the media who are writing stories about genetic or rare diseases have found the information GARD has on hand useful, accurate and complete. GARD has information on: :- What is known about a genetic or rare disease. :- What research studies are being conducted. :- What genetic testing and genetic services are available. :- Which advocacy groups to contact for a specific genetic or rare disease. :- What has been written recently about a genetic or rare disease in medical journals. GARD information specialists get their information from: :- NIH resources. :- Medical textbooks. :- Journal articles. :- Web sites. :- Advocacy groups, and their literature and services. :- Medical databases. | genetic, disease, information, genome, human, rare disease, health, physician, counselor, gene, journal, medical | has parent organization: National Institutes of Health | Office of Rare Diseases Research ; NHGRI |
nif-0000-37627 | SCR_008695 | Genetic Rare Diseases Information Center | 2026-09-12 01:00:14 | 16 | |||||||
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Pig Genome Mapping Resource Report Resource Website |
Pig Genome Mapping (RRID:SCR_012884) | PiGMaP | atlas, data or information resource, database, image collection | Map of identifyied genes controlling traits of economic and welfare significance in the pig. The project objectives were to produce a genetic map with markers spaced at approximately 20 centiMorgan intervals over at least 90% of the pig genome; to produce a physical map with at least one distal and one proximal landmark locus mapped on each porcine chromosome arm and also genetically mapped; to develop a flow karyotype for the pig based on FACS sorted chromosomes; to develop PCR based techniques to enable rapid genotyping for polymorphic markers; to evaluate synteny conservation between pigs, man, mice and cattle; to develop and evaluate the statistical techniques required to analyze data from QTL mapping experiments and to plan and initiate the mapping of QTLs in the pig; to map loci affecting traits of economic and biological significance in the pig; and to develop the molecular tools to allow the future identification and cloning of mapped loci. Animal breeders currently assume that economically important traits such as growth, carcass composition and reproductive performance are controlled by an infinite number of genes each of infinitessimal effect. Although this model is known to be unrealistic, it has successfully underpinned the genetic improvement of livestock, including pigs, over recent decades. A map of the pig genome would allow the development of more realistic models of the genetic control of economic traits and the ultimately the identification of the major trait genes. This would allow the development of more efficient marker assisted selection which may be of particular value for traits such as disease resistance and meat quality. | gene, genetic, artificial chromosome, bacteriophage, biological, carcass, cattle, cdna, comparative, disease, genome, genotype, growth, human, karyotpe, linkage, livestock, locus, map, mapping, marker, mice, molecular, p1, pig, quality, quantitative, sus scrofa, trait, yeast | has parent organization: Roslin Institute | PMID:7749223 | nif-0000-20987 | http://www.projects.roslin.ac.uk/pigmap/pigmap.html | SCR_012884 | PGM | 2026-09-12 01:00:15 | 0 | ||||||
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National Institute on Drug Abuse Center for Genetic Studies Resource Report Resource Website 1+ mentions |
National Institute on Drug Abuse Center for Genetic Studies (RRID:SCR_013061) | NIDA Center for Genetic Studies | data or information resource, data repository, data set, service resource, storage service resource | Site for collection and distribution of clinical data related to genetic analysis of drug abuse phenotypes. Anonymous data on family structure, age, sex, clinical status, and diagnosis, DNA samples and cell line cultures, and data derived from genotyping and other genetic analyses of these clinical data and biomaterials, are distributed to qualified researchers studying genetics of mental disorders and other complex diseases at recognized biomedical research facilities. Phenotypic and Genetic data will be made available to general public on release dates through distribution mechanisms specified on website. | drug abuse, family, family structure, genetic analysis, genetics, addiction, age, biomaterial, cell line, citation, clinical, clinical status, data, diagnosis, dna, genotyping, human, mental disorder, mutation analysis, phenotype, publications, sex, clinical data, genotype, gene, GWAS |
is recommended by: National Library of Medicine is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: NIH Data Sharing Repositories has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA has parent organization: Rutgers University; New Jersey; USA |
NIDA ; NIH Blueprint for Neuroscience Research |
Free, Freely available | nif-0000-00181 | https://zork5.wustl.edu//nida/ | http://zork.wustl.edu/nida/ | SCR_013061 | National Institute of Drug Abuse (NIDA) Human Genetics Initiative, NIDA Center for Genetic Studies | 2026-09-12 01:00:15 | 7 | ||||
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SNP2TFBS Resource Report Resource Website 1+ mentions |
SNP2TFBS (RRID:SCR_016885) | SNP2TFBS | data access protocol, data or information resource, database, software resource, web service | Collection of text files providing specific annotations for human single nucleotide polymorphisms (SNPs), namely whether they are predicted to abolish, create or change the affinity of one or several transcription factor (TF) binding sites. Used to investigate the molecular mechanisms underlying regulatory variation in the human genome. SNP2TFBS is also accessible over a web interface, enabling users to view the information provided for an individual SNP, to extract SNPs based on various search criteria, to annotate uploaded sets of SNPs or to display statistics about the frequencies of binding sites affected by selected SNPs. | collection, regulatory, single, polymorphism, SNP, affecting, predicted, transcription, factor, binding, site, affinity, data, human, nucleotide, genome | Swiss Institute of Bioinformatics ; Swiss National Science Foundation |
PMID:27899579 | Free, Freely available | SCR_016885 | Single Nucleotide Polymorphisms 2 Transcription Factor Binding Site, SNP2TFBS | 2026-09-12 01:00:19 | 8 | |||||||
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OMiCC Resource Report Resource Website 1+ mentions |
OMiCC (RRID:SCR_016604) | OMiCC | analysis service resource, data analysis service, data or information resource, production service resource, service resource, software resource, web application | Community based, biologist friendly web platform for creating and meta analyzing annotated gene expression data compendia., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | creating, metadata, analysis, annotated, gene, expression, data, compendia, human, mouse |
uses: Gene Expression Omnibus has parent organization: NIAID |
PMID:27323300 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016604 | OMics Compendia Commons | 2026-09-12 01:00:19 | 3 | |||||||
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YanHuang Project Resource Report Resource Website 50+ mentions |
YanHuang Project (RRID:SCR_006077) | data or information resource, database | This database presents the entire DNA sequence of the first diploid genome sequence of a Han Chinese, a representative of Asian population. The genome, named as YH, represents the start of YanHuang Project, which aims to sequence 100 Chinese individuals in 3 years. It was assembled based on 3.3 billion reads (117.7Gbp raw data) generated by Illumina Genome Analyzer. In total of 102.9Gbp nucleotides were mapped onto the NCBI human reference genome (Build 36) by self-developed software SOAP (Short Oligonucleotide Alignment Program), and 3.07 million SNPs were identified. The personal genome data is illustrated in a MapView, which is powered by GBrowse. A new module was developed to browse large-scale short reads alignment. This module enabled users track detailed divergences between consensus and sequencing reads. In total of 53,643 HGMD recorders were used to screen YH SNPs to retrieve phenotype related information, to superficially explain the donor's genome. Blast service to align query sequences against YH genome consensus was also provided. | genome, genetic, adult, chromosome, clinical, control, genomic, human, normal, FASEB list | has parent organization: BGI; Shenzhen; China | nif-0000-03654 | SCR_006077 | YH1 | 2026-09-12 01:01:40 | 53 | |||||||||
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DBETH - Database for Bacterial ExoToxins for Humans Resource Report Resource Website 1+ mentions |
DBETH - Database for Bacterial ExoToxins for Humans (RRID:SCR_005908) | DBETH | data or information resource, database | Database of Bacterial ExoToxins for Human is a database of sequences, structures, interaction networks and analytical results for 229 exotoxins, from 26 different human pathogenic bacterial genus. All toxins are classified into 24 different Toxin classes. The aim of DBETH is to provide a comprehensive database for human pathogenic bacterial exotoxins. DBETH also provides a platform to its users to identify potential exotoxin like sequences through Homology based as well as Non-homology based methods. In homology based approach the users can identify potential exotoxin like sequences either running BLASTp against the toxin sequences or by running HMMER against toxin domains identified by DBETH from human pathogenic bacterial exotoxins. In Non-homology based part DBETH uses a machine learning approach to identify potential exotoxins (Toxin Prediction by Support Vector Machine based approach). | sequence, structure, interaction network, human, pathogen, bacterial genus, toxin, bacteria, exotoxin, homology, homolog, structure, sequence, domain, prediction, mechanism, activity, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: CSIR - Indian Institute of Chemical Biology; Kolkata; India |
Council of Scientific and Industrial Research; New Delhi; India | PMID:22102573 | nlx_149481, biotools:dbeth | https://bio.tools/dbeth | SCR_005908 | Database for Bacterial ExoToxins for Humans | 2026-09-12 01:01:40 | 2 | |||||
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Kabat Database of Sequences of Proteins of Immunological Interest Resource Report Resource Website 1+ mentions |
Kabat Database of Sequences of Proteins of Immunological Interest (RRID:SCR_006465) | data or information resource, database | The Kabat Database determines the combining site of antibodies based on the available amino acid sequences. The precise delineation of complementarity determining regions (CDR) of both light and heavy chains provides the first example of how properly aligned sequences can be used to derive structural and functional information of biological macromolecules. The Kabat database now includes nucleotide sequences, sequences of T cell receptors for antigens (TCR), major histocompatibility complex (MHC) class I and II molecules, and other proteins of immunological interest. The Kabat Database searching and analysis tools package is an ASP.NET web-based portal containing lookup tools, sequence matching tools, alignment tools, length distribution tools, positional correlation tools and much more. The searching and analysis tools are custom made for the aligned data sets contained in both the SQL Server and ASCII text flat file formats. The searching and analysis tools may be run on a single PC workstation or in a distributed environment. The analysis tools are written in ASP.NET and C# and are available in Visual Studio .NET 2003/2005/2008 formats. The Kabat Database was initially started in 1970 to determine the combining site of antibodies based on the available amino acid sequences at that time. Bence Jones proteins, mostly from human, were aligned, using the now-known Kabat numbering system, and a quantitative measure, variability, was calculated for every position. Three peaks, at positions 24-34, 50-56 and 89-97, were identified and proposed to form the complementarity determining regions (CDR) of light chains. Subsequently, antibody heavy chain amino acid sequences were also aligned using a different numbering system, since the locations of their CDRs (31-35B, 50-65 and 95-102) are different from those of the light chains. CDRL1 starts right after the first invariant Cys 23 of light chains, while CDRH1 is eight amino acid residues away from the first invariant Cys 22 of heavy chains. During the past 30 years, the Kabat database has grown to include nucleotide sequences, sequences of T cell receptors for antigens (TCR), major histocompatibility complex (MHC) class I and II molecules and other proteins of immunological interest. It has been used extensively by immunologists to derive useful structural and functional information from the primary sequences of these proteins. | functional, align, alignment, amino acid, antibody, antigen, biological, cdr, chain, class i, class ii, combining, complementarity, complex, delineation, heavy, histocompatibility, human, immunological, immunological database, light, macromolecule, mhc, molecule, nucleotide, position, protein, receptor, region, sequence, structural, t cell | has parent organization: Northwestern University; Illinois; USA | nif-0000-21233 | SCR_006465 | Kabat Database | 2026-09-12 01:01:42 | 2 | |||||||||
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mitopred Resource Report Resource Website 1+ mentions |
mitopred (RRID:SCR_006135) | MITOPRED | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. It predicts nuclear-encoded mitochondrial proteins from all eukaryotic species including plants. Prediction is based on the occurrence patterns of Pfam domains (version 16.0) in different cellular locations, amino acid composition and pI value differences between mitochondrial and non-mitochondrial locations. Additionally, you may download MITOPRED predictions for complete proteomes. Re-calculated predictions are instantly accessible for proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Homo sapiens, Mus musculus and Arabidopsis species as well as all the eukaryotic sequences in the Swiss-Prot and TrEMBL databases. Queries, at different confidence levels, can be made through four distinct options: (i) entering Swiss-Prot/TrEMBL accession numbers; (ii) uploading a local file with such accession numbers; (iii) entering protein sequences; (iv) uploading a local file containing protein sequences in FASTA format. The Mitopred algorithm works based on the differences in the Pfam domain occurrence patters and amino acid composition differences in different cellular compartments. Location specific Pfam domains have been determined from the entire eukaryotic set of Swissprot database. Similarly, differences in the amino acid composition between mitochondrial and non-mitochondrial sequences were pre-calculated. This information is used to calculate location-specific amino acid weights that are used to calculate amino acid score. Similarly, pI average values of the N-terminal 25 residues in different cellular location were also determined. This knowledge-base is accessed by the program during execution. | yeast, c. elegans, drosophila, mouse, human, arabidopsis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University at Albany; New York; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mitopred, nif-0000-03956, BioTools:mitopred | https://bio.tools/mitopred, https://bio.tools/mitopred, https://bio.tools/mitopred | SCR_006135 | A genome-scale method for predicting mitochondrial proteins | 2026-09-12 01:01:41 | 7 | ||||||
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Neurocritic Resource Report Resource Website 1+ mentions |
Neurocritic (RRID:SCR_006528) | Neurocritic | blog, data or information resource, narrative resource | The Neurocritic is a blog deconstructing the most sensationalistic recent findings in Human Brain Imaging, Cognitive Neuroscience, and Psychopharmacology. Born in West Virginia in 1980, The Neurocritic embarked upon a roadtrip across America at the age of thirteen with his mother. She abandoned him when they reached San Francisco and The Neurocritic descended into a spiral of drug abuse and prostitution. At fifteen, The Neurocritic''s psychiatrist encouraged him to start writing as a form of therapy. | human, brain imaging, cognitive neuroscience, psychopharmacology, brain, imaging, neuroimaging | nlx_144592 | SCR_006528 | The Neurocritic | 2026-09-12 01:01:43 | 2 | |||||||||
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Rickettsia Genome Database Resource Report Resource Website 1+ mentions |
Rickettsia Genome Database (RRID:SCR_007102) | data or information resource, database, image | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2016. Rickettsia are obligate intracellular bacteria living in arthropods. They occasionally cause diseases in humans. To understand their pathogenicity, physiologies and evolutionary mechanisms, RicBase is sequencing different species of Rickettsia. Up to now we have determined the genome sequences of R. conorii, R. felis, R. bellii, R. africae, and R. massiliae. The RicBase aims to organize the genomic data to assist followup studies of Rickettsia. This website contains information on R. conorii and R. prowazekii. A R. conorii and R. prowazekii comparative genome map is also available. Images of genome maps, dendrogram, and sequence alignment allow users to gain a visualization of the diagrams. | evolutionary, africae, alignment, arthropod, bacteria, bellii, conorii, dendrogram, disease, genome, genomic, human, intracellular, massiliae, mechanism, pathogenicity, physiology, prowazekii, rickettsia, sequence, specie, journal article, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20993 | SCR_007102 | RicBase | 2026-09-12 01:01:45 | 1 |
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