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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
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GenomeWeb Resource Report Resource Website 1+ mentions |
GenomeWeb (RRID:SCR_000650) | GenomeWeb | blog, narrative resource, data or information resource, job resource, video resource | An independent, privately-held online and print publisher based in New York that serves the global community of scientists, technology professionals, and executives who use and develop the latest advanced tools in molecular biology research and molecular diagnostics. GenomeWeb's editorial mission is to serve readers with exclusive, in-depth coverage of the technology, institutions, and scientists that make up the worldwide research enterprise of molecular biology. We operate the largest online news organization focused on advanced research tools in genomics, proteomics, and bioinformatics. Our expert editors report and write with precision and clarity. GenomeWeb users can be found in major scientific organizations around the world, including biopharmaceutical companies, important research universities, biomedical institutes, and government laboratories. Our advertisers include leading suppliers of research tools, analytical instruments, and information technology. Getting started is easy - just register, and use your workplace e-mail address to maximize your access to content. Once you're logged in, you'll have complete free access to GenomeWeb Daily News, The Daily Scan, all of Genome Technology magazine, every GenomeWeb blog, and much more. GenomeWeb Free Content * GenomeWeb Daily News offers breaking news as well as feature articles on genomics, proteomics, bioinformatics, and more. Daily News covers not only the science and business news, but also regulatory and policy updates. Published online and twice daily by e-mail bulletin. * The Daily Scan is a roundup of the most interesting mainstream media articles, blog posts, and peer-reviewed literature relevant to genomic and proteomic scientists. Published daily online and by e-mail bulletin. * Genome Technology: GenomeWeb's magazine covers news, trends, people, and technologies in the systems biology field. It also includes Tech Guides, which feature expert troubleshooting advice on specific lab challenges, and Research Trend Digests. Published 10 times per year. Subscriptions to the print edition are free to active researchers in the US and $29 per year for non-scientists or anyone outside the US. Non-US researchers are eligible for a free subscription to the digital edition of Genome Technology. We may contact subscribers from time to time to requalify for the magazine, in compliance with our third-party readership audit. * Careers: Our Careers page includes content to help scientists in their jobs, with links to relevant external blog posts, profiles of alternative job paths, and more. Careers also includes our Job Listings board, where anyone can post job ads for free. * Cancer Minute: Updated daily and published by e-mail bulletin weekly, Cancer Minute rounds up the latest oncology peer-reviewed literature as well as news and blog posts. * Informatics Iron: This blog covers high-performance computing and the hardware side of bioinformatics, from GPUs to compute clusters and more. * The Sample: This blog focuses on a range of topics of interest to clinical labs, including the adoption of molecular tools, issues related to lab management, in-depth coverage of the major reference labs, and more. GenomeWeb Premium Content All GenomeWeb premium content provides readers with in-depth, exclusive coverage in key technology or application areas. These publications include business, technology, and research news; patent and IP information; product launches and upgrades; and hirings, promotions, and other people news. | genomics, proteomics, bioinformatics, biomedical, biopharmaceutical, genomic, molecular biology, research, rnai, scientist, technology, array, mdx, informatics, pcr, mirna, sequencing |
is used by: OncoTrack is listed by: OMICtools is parent organization of: Daily Scan |
OMICS_01731, nif-0000-10238 | SCR_000650 | GenomeWeb LLC | 2026-07-28 09:40:04 | 2 | ||||||||
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MONARCH Initiative Resource Report Resource Website 10+ mentions |
MONARCH Initiative (RRID:SCR_000824) | Monarch | data or information resource, database | Repository of information about model organisms, in vitro models, genes, pathways, gene expression, protein and genetic interactions, orthology, disease, phenotypes, publications, and authors, and ability to navigate multi-scale spatial and temporal phenotypes across in vivo and in vitro model systems in context of genetic and genomic data, using semantics and statistics. Discovery system provides basic and clinical science researchers, informaticists, and medical professionals with integrated interface and set of discovery tools to reveal genetic basis of disease, facilitate hypothesis generation, and identify novel candidate drug targets. Database that indexes authoritative information on experimental models of disease from MGI, RGD and ZFIN. | disease, animal model, phenotype, model organism, in vitro model, gene, pathway, gene expression, protein interaction, genetic interaction, orthology, disease, publication, author, genetic, genomic, model system, genotype, drug, in vivo model |
uses: Animal QTLdb uses: Ensembl Variation uses: Human Phenotype Ontology is used by: NIF Data Federation is related to: Mouse Genome Informatics (MGI) is related to: Rat Genome Database (RGD) is related to: Zebrafish Information Network (ZFIN) is related to: openSNP is related to: Ancora is related to: PhenoGen Informatics is related to: Lifespan Observations Database has parent organization: Oregon Health and Science University; Oregon; USA is parent organization of: monarch-ontologies |
NIH Office of the Director R24 OD011883 | PMID:26269093 | Free, Freely available | r3d100011594, nlx_152525, SCR_001373, nlx_152748 | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources, https://doi.org/10.17616/R31M09 | SCR_000824 | MONARCH Integrated Disease Model, MONARCH Integrated Disease Models View, MONARCH Disease Models View, The MONARCH Initiative | 2026-07-28 09:40:08 | 12 | ||||
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CoronaVIR Resource Report Resource Website 1+ mentions |
CoronaVIR (RRID:SCR_018338) | disease-related portal, data or information resource, topical portal, portal | Web based platform on COVID-19 to maintain predicted diagnostic, drug and vaccine candidates and computational resources on novel coronavirus SARS-CoV-2 and its resulting disease COVID-19. Provides collected and organized information from literature and other resources from internet, links to appropriate literature . Integrated multi-omics repository dedicated to current genomic, proteomic, diagnostic and therapeutic knowledge about coronaviruses. | COVID-19, SARS-CoV-2, diagnostic, drug, candidate, computational resource. coronavirus, disease, literature, genomic, proteomic, data | COVID-19 | DOI:10.31219/osf.io/xegzu | Free, Freely available | SCR_018351 | SCR_018338 | 2026-07-28 09:44:44 | 4 | ||||||||
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MitoRes Resource Report Resource Website 1+ mentions |
MitoRes (RRID:SCR_008208) | MitoRes | software application, data analysis software, software resource, data processing software, data acquisition software | MitoRes, is a comprehensive and reliable resource for massive extraction of sequences and sub-sequences of nuclear genes and encoded products targeting mitochondria in metazoa. It has been developed for supporting high-throughput in-silico analyses aimed to studies of functional genomics related to mitochondrial biogenesis, metabolism and to their pathological dysfunctions. It integrates information from the most accredited world-wide databases to bring together gene, transcript and encoded protein sequences associated to annotations on species name and taxonomic classification, gene name, functional product, organelle localization, protein tissue specificity, Enzyme Classification (EC), Gene Ontology (GO) classification and links to other related public databases. The section Cluster, has been dedicated to the collection of data on protein clustering of the entire catalogue of MitoRes protein sequences based on all versus all global pair-wise alignments for assessing putative intra- and inter-species functional relationships. The current version of MitoRes is based on the UniProt release 4 and contains 64 different metazoan species. The incredible explosion of knowledge production in Biology in the past two decades has created a critical need for bioinformatic instruments able to manage data and facilitate their retrieval and analysis. Hundreds of biological databases have been produced and the integration of biological data from these different resources is very important when we want to focus our efforts towards the study of a particular layer of biological knowledge. MitoRes is a completely rebuilt edition of MitoNuc database, which has been extensively modified to deal successfully with the challenges of the post genomic era. Its goal is to represent a comprehensive and reliable resource supporting high-quality in-silico analyses aimed to the functional characterization of gene, transcript and amino acid sequences, encoded by the nuclear genome and involved in mitochondrial biogenesis, metabolism and pathological dysfunctions in metazoa. The central features of MitoRes are: # an integrated catalogue of protein, transcript and gene sequences and sub-sequences # a Web-based application composed of a wide spectrum of search/retrieval facilities # a sequence export manager allowing massive extraction of bio-sequences (genes, introns, exons, gene flanking regions, transcripts, UTRs, CDS, proteins and signal peptides) in FASTA, EMBL and GenBank formats. It is an interconnected knowledge management system based on a MySQL relational database, which ensures data consistency and integrity, and on a Web Graphical User Interface (GUI), built in Seagull PHP Framework, offering a wide range of search and sequence extraction facilities. The database is compiled extracting and integrating information from public resources and data generated by the MitoRes team. The MitoRes database consists of comprehensive sequence entries whose core data are protein, transcript and gene sequences and taxonomic information describing the biological source of the protein. Additional information include: bio-sequences structure and location, biological function of protein product and dynamic links to both, external public databases used as data resources and public databases reporting complementary information. The core entity of the MitoRes database is represented by the protein so that each MitoRes entry is generated for each protein reported in the UniProt database as a nuclear encoded protein involved in mitochondrial biogenesis and function. Sponsors: MitoRes has been supported by Ministero Universit e Ricerca Scientifica, Italy (PRIN, Programma Biotecnologie legge 95/95-MURST 5, Proiect MURST Cluster C03/2000, CEGBA). Currently it is supported by operating grants from the Ministero dellIstruzione, dellUniversit e della Ricerca (MIUR), Italy (PNR 2001-2003 (FIRB art.8) D.M. 199, Strategic Program: Post-genome, grant 31-063933 and Project n.2, Cluster C03 L. 488/929). | dysfunction, encode, enzyme, exon, extraction, function, functional, gene, alignment, amino acid, biogenesis, bioinformatic, biological, biology, cds, classification, disfunctional, genome, genomic, genomics, intron, localization, location, metabolic process, metabolism, metazoa, mitochondria, mitochondrial, mitochondrial genes and proteins databases, nuclear, nuclear_gene, nuclear_mitochondrial, nuclear_sequence, organelle, organelle localization, pathological, peptide, protein, protein_coding, protein structure classification, region, sequence, signal, signal_peptide, specie, specificity, structure, sub-sequence, taxonomic, tissue, transcript, utr | nif-0000-21269 | http://www2.ba.itb.cnr.it/MitoNuc/ | SCR_008208 | 2026-07-28 09:42:05 | 1 | |||||||||
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Parasite genome databases and genome research resources Resource Report Resource Website 1+ mentions |
Parasite genome databases and genome research resources (RRID:SCR_008150) | database, data or information resource, topical portal, portal | This website contains information about the genomic sequence of parasites. It also contains multiple search engines to search six frame translations of parasite nucleotide databases for motifs, parasite protein databases for motifs, and parasite protein databases for keywords and text terms. * Guide to Internet Access to Parasite Genome Information * Guide to web-based analysis tools * Parasite Genome BLAST Server: Search a range of parasite specific nucleotide sequence databases with your own sequence. * Parasite Proteome Keyword Search Facility: Search parasite protein databases for keywords and text terms * Parasite Proteome Motif Search Facility: Search parasite protein databases for motifs * Parasite Six Frame Translation Motif Search Facility: Search six frame translations of parasite nucleotide databases for motifs * Genome computing resources: A list of ftp and gopher sites where genome computing applications and other resources can be found. | genome, genomic, nucleotide, parasite, protein, proteome, sequence, gold standard | has parent organization: European Bioinformatics Institute | nif-0000-20981 | SCR_008150 | Parasite Genome Database | 2026-07-28 09:42:01 | 2 | |||||||||
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University of California Davis Center for Comparative Medicine Resource Report Resource Website |
University of California Davis Center for Comparative Medicine (RRID:SCR_008294) | data or information resource, organization portal, department portal, portal | The University of California Davis Center for Comparative Medicine (CCM) is a cooperative, interdisciplinary research and teaching center that is co-sponsored by the School of Medicine and the School of Veterinary Medicine. CCM Faculty members have academic appointments in one or both Schools. The CCM Research Mission is to investigate the pathogenesis of human and animal disease, using animal models or naturally occurring animal diseases. Areas of emphasis include host-agent interactions during infectious disease, intervention and prevention strategies for infectious diseases, cancer, and mouse biology. CCM faculty contribute a broad range of expertise to these areas, including the disciplines of immunology, genomics, pathology, biochemistry, physiology, microbiology, molecular virology, and informatics. Through its robust and interdisciplinary research programs, the CCM provides a rich academic environment for teaching at the professional, graduate, and post-graduate levels within the School of Medicine and School of Veterinary Medicine. Opportunities are available for professional students from both schools to gain research experience. PhD candidates can pursue training opportunities in the CCMs faculty-sponsored research laboratories, with support from a number of training grants. This diverse research environment is intended to attract and train high-quality candidates to the disciplines of comparative medicine, independent and collaborative research, and mouse biology. Sponsors: CCM is supported by UC Davis. | animal, biochemistry, biology, cancer, comparative, disease, genomic, immunology, infectious, informatic, medicine, microbiology, molecular, mouse, pathology, physiology, research, veterinary, virology | has parent organization: University of California at Davis; California; USA | nif-0000-24374 | SCR_008294 | CCM | 2026-07-28 09:42:07 | 0 | |||||||||
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BioBank Central Resource Report Resource Website |
BioBank Central (RRID:SCR_008645) | BioBank Central | service resource, biospecimen repository, material storage repository, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 27, 2013. Web-based portal to connect all the constituencies in the global biobank community. The project seeks to increase the transparency and accessibility of the scientific research process by connecting researchers with an additional source of funding - microinvestments received from the broader online community. In exchange for these public investments, researchers will maintain research logs detailing the play-by-play progress made in their project, as well as publishing all of their data in a public database under a science commons license. These research projects, in turn, will serve to continually update a research-based neuroscience-based human brain & body curriculum. Biobanks are the meeting point of two major information trends in biomedical research: the generation of huge amounts of genomic and other laboratory data, and the electronic capture and integration of patient clinical records. They are comprised of large numbers of human biospecimens supplemented with clinical data. Biobanks when implemented effectively can harness the power of both genomic and clinical data and serve as a critical bridge between basic and applied research, linking laboratory to patient and getting to cures faster. As science and technology leaders work to address the many challenges facing U.S. biobanks logistical, technical, ethical, financial, intellectual property, and IT BioBank Central will serve as an accurate and timely source of knowledge and news about biorepositories and their role in research and drug development. The Web site also provides a working group venue, patient and public education programs, and a forum for international collaboration and harmonization of best practices. | biobank, community, biomedical, data, genomic, integration, patient, clinical, human, biospecimen, science, technology, biorepository, drug, development, education | has parent organization: Open Source Science Project | FasterCures ; Feinstein Kean Healthcare ; IBM Healthcare and Life Sciences ; Affymetrix ; Bioaccelerate Holdings Inc. ; Invitrogen Corporation |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-32933 | SCR_008645 | 2026-07-28 09:42:22 | 0 | |||||||
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genes2mind Resource Report Resource Website 1+ mentions |
genes2mind (RRID:SCR_008872) | genes2mind | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | genes2mind is a tool for rapid exploratory analysis of psychotropic drug-induced gene expression in the brain. We present here an open resource containing comparison of effects of various classes of psychotropic drugs on transcriptional alterations of ~20,000 genes in the mouse brain (C57BL/6J). Data stored in the database include raw gene expression values as well as results of drug comparison. * Genomic Signature Identification section allows for the identification of drug-specific genomic signatures. * Genomic Signature Analysis section allows for further inspection and visualization of the signatures using multidimensional data analysis (PCA), co-expression analysis and heatmaps. * Single Gene Inspection allows for brief review of expression of specific candidate genes using barplots. | psychotropic drug, gene expression, gene, brain, drug, c57bl/6j, genomic | has parent organization: Polish Academy of Sciences Poznan; Poznan; Poland | Institute of Pharmacology PAS ; Polish Ministry of Science and Higher Education DeMeTer 3.1 POIG; Polish Ministry of Science and Higher Education NN405 274137; European Union FP6 GENADDICT LSHM-CT-2004-005166 |
nlx_149344 | SCR_008872 | 2026-07-28 09:42:17 | 3 | ||||||||
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ALLELIX Resource Report Resource Website 1+ mentions |
ALLELIX (RRID:SCR_009115) | ALLELIX | software application, service resource, data analysis service, software resource, production service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 23, 2013. Software application / data analysis service where one can enter the alleles of commonly used STR by clicking the mouse. The algorithm calculates the paternity index and the Essen-Moeller probability of kinship for the deficiency- and the trio case. Everybody can use the network-software online after registering. The usage on the internet is free. Academic users can ask me to unlock an option to display the details (formulas/frequencies etc.) and to have an export-funktion to MS Word. The program is in German and (non-professional) English. An expansion to other languages is easy, if somebody helps us with the translation. For those who are interested to have the software running on their own intranet (for database security reasons) an individual agreement can be found. (entry from Genetic Analysis Software) (German version is: http://www.allelix.de) | gene, genetic, genomic, c++, java script, ms-windows, (2000 &iis/me & personal webserver) | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154216 | SCR_009115 | Allelix - Paternity Linkage Analysis Online | 2026-07-28 09:42:17 | 2 | |||||||
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CMAP Resource Report Resource Website 100+ mentions |
CMAP (RRID:SCR_009034) | CMap | software application, data analysis software, software resource, data processing software | Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, unix, solaris, freebsd, linux, sequence, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SoftCite has parent organization: Generic Model Organism Database Project works with: Drug Gene Budger |
PMID:19648141 | GNU General Public License | nlx_153998, OMICS_00933 | https://sourceforge.net/projects/gmod/files/cmap/ | http://www.gmod.org/cmap/, http://gmod.org/wiki/Cmap | SCR_009034 | , GMOD Comparative Mapping (CMap) tool, Comparative Mapping tool, genetic and comparative maps | 2026-07-28 09:42:19 | 413 | ||||
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DETONATE Resource Report Resource Website 1+ mentions |
DETONATE (RRID:SCR_017035) | DETONATE | software application, data analysis software, sequence analysis software, software resource, data processing software | Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences. | evaluate, de novo, transcriptome, assembly, RNAseq, data, RSEM-EVAL, REF-EVAL, dataset, genomic, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
NHGRI R01 HG005232; NLM T15 LM007359 |
PMID:25608678 | Free, Available for download, Freely available | biotools:detonate | https://bio.tools/detonate | SCR_017035 | DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation, DETONATE | 2026-07-28 09:44:30 | 2 | ||||
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Eutherian comparative genomic analysis protocol Resource Report Resource Website 10+ mentions |
Eutherian comparative genomic analysis protocol (RRID:SCR_014401) | data or information resource, data set, protocol | Eutherian comparative genomic analysis protocol as one framework of eutherian gene data set revisions. Protocol integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis with 3 new tests including test of reliability of public eutherian genomic sequences using genomic sequence redundancies, test of contiguity of public eutherian genomic sequences using multiple pairwise genomic sequence alignments and test of protein molecular evolution using relative synonymous codon usage statistics. Public eutherian reference genomic sequence data sets. | eutheria, gene, data set, annotation, genomic, molecular, evolution, phylogenetic, analysis protocol |
has parent organization: Australian National University; Acton; Australia works with: European Nucleotide Archive (ENA) |
DOI:10.1016/j.genrep.2019.100414 | Free, Freely available | https://doi.org/10.1016/j.dib.2015.11.056 | SCR_014401 | 2026-07-28 09:43:28 | 15 | ||||||||
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LDHEATMAP Resource Report Resource Website 100+ mentions |
LDHEATMAP (RRID:SCR_006312) | software application, software resource | Software application that plots measures of pairwise linkage disequilibria for SNPs (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154424, SCR_009347, nlx_154561 | http://stat-db.stat.sfu.ca:8080/statgen/research/LDheatmap | SCR_006312 | R/LDHEATMAP | 2026-07-28 09:41:33 | 160 | ||||||||
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Gene Regulation Ontology Resource Report Resource Website |
Gene Regulation Ontology (RRID:SCR_010590) | GRO, BOOTStrep | controlled vocabulary, data or information resource, ontology | Ontology that is a conceptual model for the domain of gene regulation. It covers processes that are linked to the regulation of gene expression as well as physical entities that are involved in these processes (such as genes and transcription factors) in terms of ontology classes and semantic relations between classes. GRO is intended to represent common knowledge about gene regulation in a formal way rather than representing extremely fine-grained classes as can be found in ontologies such as the Gene Ontology (GO) (created for data base annotation purposes) and various relevant databases. The main purpose of the ontology is to support NLP applications. It has a particular focus on the relations between processes and the molecules (participants) involved. The basic structure of the GRO is a direct acyclic graph (DAG) with ontology classes as nodes and is-a relations between classes as edges. The taxonomic backbone is further enriched by several semantic relation types (part-of, from-species, participates-in with the two sub-relations agent-of and patient-of). | owl, genomic, proteomic, biological process, gene regulation, gene expression, gene, transcription factor, process, molecule, biological_process |
is listed by: BioPortal is listed by: OBO has parent organization: European Bioinformatics Institute |
nlx_157415, nlx_46399 | http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html, http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO_latest | SCR_010590 | Gene Regulation Ontology - Ontological resource from the BOOTStrep project for the representation of gene regulation events | 2026-07-28 09:42:49 | 0 | |||||||
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MOgene Resource Report Resource Website 50+ mentions |
MOgene (RRID:SCR_012433) | MOgene | access service resource, service resource, commercial organization, core facility | Core provides services to its partners in deploying genomic capabilities to bring critical solutions to both agriculture and industrial biotech operations. Core facility also provides assistance to research, biotech/pharma and government facilities. In addition to being an Agilent Certified Service Provider MOgene is also a CLIA certified genomics service facility offering one stop service and solution from Tissue/Cells to Analysis. Core offers RNA/DNA isolation, Microarrays, NextGen sequencing, Real time PCR and bioinformatics services. | genomic, sequencing, genotyping, microarray, isolation | is listed by: ScienceExchange | SciEx_13293 | http://www.scienceexchange.com/facilities/mogene-lc | SCR_012433 | MOgene LC, MOgene.com | 2026-07-28 09:43:03 | 64 | |||||||
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Center for Disease Control and Prevention: Genetic Testing Reference Materials Coordination Program Resource Report Resource Website 1+ mentions |
Center for Disease Control and Prevention: Genetic Testing Reference Materials Coordination Program (RRID:SCR_013029) | data or information resource, topical portal, portal | The goal of the Genetic Testing Reference Materials Coordination Program (GeT-RM) is to coordinate a self-sustaining community process to improve the availability of appropriate and characterized reference materials for: Quality control (QC), Proficiency testing (PT), Test development & validation, Research. The purpose of this program is: - To help the genetic testing community obtain appropriate and characterized reference materials - To facilitate and coordinate information exchange between users and providers of QC and reference materials - To coordinate efforts for contribution, development, characterization and distribution of reference materials for genetic testing Get-RM provides information about cell lines, DNA, and other kinds of materials that could be used as reference materials for molecular genetic testing. Some of these materials have been characterized by the GeT-RM program and can be divided into three categories: - Genetic Inherited Disease & Pharmacogenetics This section includes information about cell lines, DNA, and other samples that can be used as reference materials for various inherited diseases (including cystic fibrosis, fragile X, Huntington disease, and Ashkenazi Jewish-related diseases), pharmacogenetic loci, and biochemical genetics. The GeT-RM program has confirmed the genotype of many of the genomic DNA samples through testing in multiple clinical genetic laboratories. - Molecular Oncology This section includes information about commercially available cell lines, DNA, and other kinds of materials that could be used as reference materials for various types of cancers, including leukemia/lymphoma and solid tumors. - Infectious Disease This section includes information about commercially available cell lines, DNA, and other kinds of materials that could be used as reference materials for various infectious disease pathogens including viruses, bacteria, and protozoa. | fragile x, genetic, genetics, genetic testing, ashkenazi, bacteria, biochemical, cancer, cell, cell line, coordination, cystic fibrosis, development, disease, dna, genomic, genotype, huntington disease, inherited, jewish, leukemia, locus, lymphoma, material, molecular, oncology, pathogen, pharmacogentic, protozoa, quality, solid, testing, tumor, virus | has parent organization: Centers for Disease Control and Prevention | nif-0000-10189 | SCR_013029 | CDC GeT-RM Program | 2026-07-28 09:43:10 | 3 | |||||||||
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SIFT Resource Report Resource Website 10000+ mentions |
SIFT (RRID:SCR_012813) | SIFT | service resource, data analysis service, data access protocol, software resource, source code, production service resource, web service, analysis service resource | Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available. | gene, genetic, genomic, amino acid, substitution, protein function, coding region, single nucleotide variant, coding indel, deletion, insertion, sequence, protein, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SIFT 4G has parent organization: Genome Institute of Singapore; Singapore; Singapore has parent organization: J. Craig Venter Institute |
Agency for Science Technology and Research ; NIGMS GM29009 |
PMID:19561590 PMID:12824425 PMID:11337480 DOI:10.1038/nprot.2009.86 |
Non-commercial | biotools:sift, OMICS_00137, nlx_154618 | http://sift.jcvi.org/, https://bio.tools/sift, https://sources.debian.org/src/sift/ | http://sift.bii.a-star.edu.sg/SIFT.html | SCR_012813 | Sorting Intolerant From Tolerant | 2026-07-28 09:43:10 | 10223 | |||
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eQTL Visualization Tool Resource Report Resource Website 1+ mentions |
eQTL Visualization Tool (RRID:SCR_013413) | data visualization software, software resource, software application, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. eQTL Explorer was developed as a computational resource to visualize and explore data from combined genome-wide expression and linkage studies is essential for the development of testable hypotheses. This visualization tool stores expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface. eQTL Explorer also provides a new and powerful tool to interrogate these very large and complex datasets. eQTLexplorer allows users to mine and understand data from a repository of genetical genomics experiments. It will graphically display eQTL information based on a certain number of selection criteria, including: tissue type, p-value, cis/trans, probeset Affymetrix id and PQTL type. Sponsors: This work was funded by the MRC Clinical Sciences Centre and the Wellcome Trust programme for Cardiovascular Functional Genomics. | experiment, explore, expression, genome, genetic, genetical, cis, computational, data, database, genomic, grafical, interface, linkage, mine, pqtl type, p-value, repository, tissue, tissue type, trans, visualization, visualize | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10222 | SCR_013413 | eQTLexplorer | 2026-07-28 09:43:28 | 1 | |||||||||
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Genetic Analysis Software Resource Report Resource Website 1+ mentions |
Genetic Analysis Software (RRID:SCR_013155) | GAS | data set, data or information resource, catalog, database, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Listing of computer software for the gene mapping community on the following topics: genetic linkage analysis for human pedigree data, QTL analysis for animal/plant breeding data, genetic marker ordering, genetic association analysis, haplotype construction, pedigree drawing, and population genetics. The inclusion of a program should not be interpreted as an endorsement to that program from us. In the last few years, new technology produces new types of genetic data, and the scope of genetic analyses change dramatically. It is no longer obvious whether a program should be included or excluded from this list. Topics such as next-generation-sequencing (NGS), gene expression, genomics annotation, etc. can all be relevant to a genetic study, yet be specialized topics by themselves. Though programs on variance calling from NSG can be in, those can sequence alignment might be out; programs on eQTL can be in, those on differential expression might be out. This page was created by Dr. Wentian Li, when he was at Columbia University (1995-1996). It was later moved to Rockefeller University (1996-2002), and now takes its new home at North Shore LIJ Research Institute (2002-now). The present copy is maintained by Jurg Ott as a single file. More than 240 programs have been listed by December 2004, more than 350 programs by August 2005, close to 400 programs by December 2006, and close to 480 programs by November 2008, and over 600 programs by October 2012. A version of the searchable database was developed by Zhiliang Hu of Iowa State University, and a recent round of updating was assisted by Wei JIANG of Harbin Medical School. Some earlier software can be downloaded from EBI: ftp://ftp.ebi.ac.uk/pub/software/linkage_and_mapping/ (Linkage and Mapping Software Repository), and http://genamics.com/software/index.htm may contain archived copy of some programs. | gene mapping, gene, genetic, genomic, model, modeling, software program, genetic linkage analysis, qtl analysis, genetic marker order, genetic association analysis, haplotype construction, pedigree drawing, population genetics |
is used by: NIF Data Federation lists: EM-DECODER lists: ENTROPY BLOCKER lists: SOAP lists: ADEGENET lists: 2LD lists: SQTL lists: POLYMORPHISM lists: EDAC lists: FEST lists: GENEHUNTER SAD lists: COMDS lists: CHAPLIN lists: CRIMAP lists: DCHIP LINKAGE lists: FLOSS lists: HAP 1 lists: HAPSCOPE lists: LDB/LDB+ lists: LOCUSMAP lists: MRH lists: PEDIGREE-VISUALIZER lists: PEDPHASE lists: QTL CAFE lists: RHMAPPER lists: R/GC, R/GCF lists: R/GWAPOWER lists: R/WEIGHTED FDR lists: SIMM lists: SOLAR lists: TDTHAP lists: HWESTRATA lists: TDT-PC lists: EQTL EXPLORER lists: GAS2 lists: LDMET lists: LAMBDAA lists: EIGENSOFT/EIGENSTRAT lists: Happy lists: LAMP lists: CLUSTAG lists: OSA lists: SIMIBD lists: SNPSTATS lists: Haploview lists: QGene lists: PAWE-3D lists: MILD lists: PEDPLOT lists: GS-EM lists: PEDSCRIPT lists: Multipoint Identical-by-descent Method lists: PARENTE lists: Integrated Software lists: PEDRAW/WPEDRAW lists: POPDIST lists: TDTASP lists: TDTPOWER lists: TDT/S-TDT lists: HAPLOBLOCKFINDER lists: HAPMIXMAP lists: Genotype-IBD Sharing Test lists: LDGROUP lists: LDHAT lists: LDMAP lists: LDHEATMAP lists: LDSELECT lists: LINKAGE lists: LDSUPPORT lists: FASTLINK lists: LINKAGE - CEPH lists: LSP lists: Whap lists: TREESCAN lists: Graphical Overview of Linkage Disequilibrium lists: MAIA lists: MULTIMAP lists: R/ADEGENET lists: R/ENTROPY BLOCKER lists: BEAM lists: BMAPBUILDER lists: POPGEN lists: RTDT lists: R/SPECTRAL-GEM lists: R/STEPWISE lists: HAPLOCLUSTERS lists: TKMAP lists: CLUMP lists: FAMOZ lists: INTEGRAYEDMAP lists: SIBMED lists: POOLSCORE lists: LDA lists: LAPSTRUCT lists: BETA lists: ALTree lists: TRANSMIT lists: ETDT lists: R/TDTHAP lists: RVTESTS lists: S lists: ET-TDT lists: ILR lists: MAPCREATOR lists: MAPMAKER/SIBS lists: MAP MANAGER QT lists: MGA-MAPF2 lists: Pedigree-Draw lists: FASTMAP (1) lists: ASPEX lists: PEDJAVA lists: PEDPEEL lists: SIMCOAL lists: SNPHAP lists: SNPHARVESTER lists: SNP-HWE lists: TAGSNP lists: FASTMAP (2) lists: FASTSLINK lists: GASP lists: GENOGRAM-MAKER lists: GENEHUNTER++SAD lists: GENEPI.JAR lists: BDGEN lists: TLINKAGE lists: GENOME lists: EASYPOP lists: GENOMESIMLA lists: TRAP lists: CARTHAGENE lists: ACT lists: ADMIXMAP lists: 2DMAP lists: ALBERT lists: 2SNP lists: AGEINF lists: ALLASS lists: PEDIGREEQUERY lists: PATH lists: MULTIQTL lists: SPERMSEG lists: FASTER lists: Platypus lists: KIN lists: SNP ASSISTANT lists: GRONLOD lists: COMBIN lists: ARLEQUIN lists: SEGPATH lists: JENTI lists: SCOUT lists: HAPLOREC lists: UNPHASED lists: POWER lists: HAPLO 1 lists: HAPLO 2 lists: CHIP2SPELL lists: MAP MANAGER QTX lists: G-MENDEL lists: ASSOCIATIONVIEWER lists: WHICHRUN lists: GENECLASS lists: MAREYMAP lists: HELIXTREE lists: SVCC lists: GENEHUNTER-MODSCORE lists: FAMHAP lists: BAMA lists: WEBQTL lists: HAPLOVISUAL lists: CASPAR lists: GC/GCF lists: MIXSCORE lists: POWQ lists: QTLNetwork lists: SIMULAPLOT lists: SQTDT/SPDT lists: FESTA lists: BOTTLENECK lists: PAP lists: QUANTO lists: R/QTL lists: SNPEM lists: GENEPOOL lists: EPISTACY lists: VITESSE lists: LEA lists: DMAP lists: MOSCPHASER lists: UMAKE lists: TDT-AE lists: HAPLOWSER lists: STEPC lists: RECORD lists: QUTIE lists: R/COMPOSITELD lists: FINESSE lists: R/EHP lists: R/HCLUST lists: STEPWISE lists: genehunter-imprinting lists: PBAT lists: R/BARS lists: HARDY lists: R/ARP.GEE lists: R/COVIBD lists: STRAT lists: TREELD lists: TUNA lists: SIBSIM lists: IGG lists: ALLELIX lists: ALLEGRO lists: ALOHOMORA lists: ALP lists: AMELIA lists: ANALYZE lists: ANCESTRY lists: APE lists: BARS lists: APL-OSA lists: APM lists: ARIEL lists: GENOMIZER lists: ASP/ASPSHARE lists: BIMBAM lists: BIOIDE lists: BIOLAD-DB lists: BLADE lists: BLOCK lists: BOOLD lists: BOOSTRAPPER lists: BPPH lists: BQTL lists: DNABASER lists: Calculator for Association with Two Stage design lists: CC-QLS lists: CCRAVAT lists: CCREL lists: CEPH2CRI lists: CEPH2MAP lists: EVOKER lists: CFC lists: CHECKHET lists: MATLINK lists: CHECKMATRIX lists: CHIAMO lists: CHROMOSCAN lists: CHROMOSEG lists: COPE lists: HCLUST lists: COVIBD lists: CRIMAP-PVM lists: CROSSFIND lists: DGENE lists: EHPLUS lists: DHSMAP lists: DISENTANGLER lists: MAKEPED lists: DOLINK lists: DPPH lists: GREGOR lists: EAGLET lists: EASYLINKAGE/EASYLINKAGE-PLUS lists: EH lists: EHAP lists: EHP lists: EMLD lists: EPDT lists: ERPA lists: EXOMEPICKS lists: R/META lists: FASTEHPLUS lists: FASTLINK lists: FBAT lists: FINETTI lists: FIRSTORD lists: FISHER lists: GAIA lists: GAP lists: GAS lists: GCHAP lists: GDA lists: GEMS lists: GENECOUNTING lists: GENEFINDER lists: GENEHUNTER lists: GENEHUNTER-IMPRINTING lists: GENEHUNTER-PLUS lists: GENEPOP lists: GENERECON lists: GENESPRING GT lists: GENIE lists: GENETIC POWER CALCULATOR lists: GENETSIM lists: GENOOM lists: GENEVAR lists: GENEWEAVER lists: GENOCHECK lists: GENOPROOF lists: GENTOOLS lists: GEST lists: GEVALT lists: GGT lists: GHOST lists: GLIDERS lists: GLUE lists: GMA lists: GMCHECK lists: GSMA lists: GTOOL lists: GWAPOWER lists: HAP 2 lists: HAPAR lists: HAPASSOC lists: HAPBLOCK lists: HAPGEN lists: HAPINFERX lists: HAPLOBLOCK lists: HAPLOBUILD lists: HAPLOPOOL lists: HAPLORE lists: HAPLO.STAT lists: HAPLOT lists: HAPLOTTER lists: TWOLOC lists: HAPLOTYPE ESTIMATION lists: HAPLOTYPER lists: HAPMINER lists: HAP-SAMPLE lists: HAPSIMU lists: HIT lists: HOMOG/HOMOGM lists: HOTSPOTTER lists: HPLUS lists: HS-TDT lists: HTR lists: HTSNPER lists: MDR-PDT lists: INTERSNP lists: IMPUTE lists: NOPAR lists: JLIN lists: JOINMAP lists: JPSGCS lists: J/QTL lists: KING lists: LAMARC lists: LINKAGE-IMPRINT lists: LINKBASE lists: LIPED lists: LNKTOCRI lists: LOCUSZOOM lists: LOGINSERM ESTIHAPLO lists: LOH-LINKAGE lists: LOKI lists: LOT lists: L-POP lists: LRP lists: LRTAE lists: LTSOFT lists: MADMAPPER lists: Marker And Gene Interpolation and Correlation lists: MALDSOFT lists: MAMA lists: MANTEL-STRUCT lists: MAP/MAP+/MAP+H/MAP2000 lists: MAPCHART lists: MIDAS lists: MAPDISTO lists: MAPDRAW lists: MAPINSPECT lists: MAPL lists: MARGARITA lists: MDBLOCKS lists: MAPMAKER/EXP lists: MAPMAKER/HOMOZ lists: MAPMAKER/QTL lists: MAPQTL lists: MCQTL lists: MEGA2 lists: MEGASNPHUNTER lists: MENDEL lists: MERLIN lists: MFLINK lists: MINIMAC lists: MINSAGE lists: MITPENE lists: MKGST lists: MMDRAWER lists: MLBGH lists: MLD lists: MLR-TAGGING lists: PEDMANAGER lists: SAGE lists: MPDA lists: MULTIDISEQ lists: MULTIMAPPER lists: MULTIMAPPER/OUTBRED lists: MULTIPOPTAGSELECT lists: MULTISIM lists: MUTAGENESYS lists: NOCOM lists: NUCULAR lists: ONEMAP lists: OSIRIS lists: P ACT lists: PASS PEDIGREE lists: PAWE lists: PDA lists: PDPSYS lists: PDT lists: PED lists: PEDAGREE lists: PEDCHECK lists: PEDSTATS lists: PEDSYS lists: PEDVIZAPI lists: PEER lists: PHASE lists: PLABSIM lists: PL-EM lists: POINTER lists: POOL STR lists: POWERMARKER lists: POWERTRIM lists: POWTEST lists: PREPLINK lists: PREST lists: PROBMAX lists: PROC QTL lists: PROFILER lists: PRT lists: PSAT lists: SAS/GENETICS lists: PSEUDO lists: PSEUDOMARKER lists: PSEUDOMARKER.M lists: R/LDHEATMAP lists: QTL-ALL lists: QTL Cartographer lists: QTL EXPRESS lists: QU-GENE lists: RISCALW lists: RC-TDT lists: REAPER lists: RELATIVE lists: RELATIVEFINDER lists: RELCHECK lists: RELPAIR lists: RELTYPE lists: RHMAP lists: ROMPREV lists: ROSATTA SYLLEGO SYSTEM lists: R/GAP lists: R/HAPASSOC lists: R/IBDREG lists: R/LAPSTRUCT lists: R/LDGROUP lists: R/LUCA lists: R/METASIM lists: R/ONEMAP lists: R/PIAGE lists: R/POOLSCORE lists: R/POPGEN lists: R/QTLBIM lists: R/SNP.PLOTTER lists: SDMINP lists: SELSIM lists: SEQUENCE LD/SEQUENCE LDHOT lists: SIBERROR lists: SIBLINK lists: SIB-PAIR lists: SILCLOD lists: SIMLA lists: SNP CHART lists: SIMLINK lists: SIMPED lists: SIMPLE lists: SIMULA lists: SIMULATE lists: SIMUPOP lists: SIMWALK lists: START lists: SKAT lists: SLINK lists: SMOOTH lists: Suite of Nucleotide Analysis Programs lists: SNAP 3 lists: SNPALYZE lists: SNPFILE lists: SNPLINK lists: SNPP lists: SNP.PLOTTER lists: SNPTEST lists: SPAM lists: SPECTRAL-GEM lists: SPERM lists: SPIP lists: SPLAT lists: TAGSTER lists: SPLINK lists: SSAHASNP lists: SUMSTAT lists: SUP lists: SWEEP lists: TAGGER lists: TFPGA lists: TREESELECT lists: UNKNOWN lists: UTIL lists: WHAIT lists: ZAPLO lists: HAPBLOCK 2 lists: PLABQTL lists: TASSEL lists: MCLEEPS lists: SASGENE lists: PANGAEA lists: TOMCAT lists: SCORE-SEQ lists: SASQUANT lists: QMSIM lists: PIAGE lists: PEDPACK lists: INSEGT lists: IBDREG lists: GLFSINGLE/GLFTRIO/GLFMULTIPLES lists: GGSD lists: ECLIPSE lists: CHROMSCAN lists: COMPOSITELD lists: BOOST lists: ARP.GEE lists: BOREL lists: GASSOC lists: MENDELSOFT lists: PLINK/SEQ lists: POLYPHEN lists: SPREG lists: MOLKIN lists: PRESTO: Genetic Association Analysis Software lists: ENDOG lists: BEAGLECALL lists: GWASELECT lists: HEGESMA lists: SNIPPEEP lists: TAGIMPUTE lists: SNPMSTAT lists: SNP HITLINK lists: MECPM lists: R/FEST lists: MAOS lists: SUPERLINK lists: PEDFIDDLER lists: VG lists: HAPSTAT lists: QTDT lists: GRIDQTL lists: VH lists: R/QTLDESIGN lists: PyPop lists: ANTMAP lists: MDR lists: WEIGHTED FDR lists: THESIAS lists: DMLE lists: SGS lists: BAYESFST lists: HWMET lists: GRR lists: AUTOSCAN lists: TRIMHAP lists: ILLUMINUS lists: PELICAN lists: HAPLOPAINTER lists: HOMOZYGOSITYMAPPER lists: GERMLINE lists: PLINK lists: MACH 1.0 lists: BEAGLE lists: BIRDSUITE lists: BREAKDANCER lists: CAROL lists: CASAVA lists: CYRILLIC lists: DINDEL lists: GenABEL lists: GATK lists: PEDIGRAPH lists: MADELINE lists: METAL lists: OLORIN lists: PEDHUNTER lists: POLYMUTT lists: SAMTOOLS lists: SNAP - SNP Annotation and Proxy Search lists: STRUCTURE lists: SVA lists: SYZYGY lists: VAAST lists: Hapmix lists: Ancestrymap lists: Hmmer lists: PROGENY lists: VarScan lists: MORGAN lists: CMAP lists: SIMHAP lists: SIFT lists: ANNOVAR lists: Body Mass Index Calculator lists: PolyPhen: Polymorphism Phenotyping has parent organization: Feinstein Institute for Medical Research has parent organization: Iowa State University; Iowa; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33506 | http://lab.rockefeller.edu/ott/geneticsoftware | http://linkage.rockefeller.edu/soft/ | SCR_013155 | An Alphabetic List of Genetic Analysis Software | 2026-07-28 09:43:13 | 9 | |||||
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Blixem Resource Report Resource Website 1+ mentions |
Blixem (RRID:SCR_015994) | software application, software resource, data processing software, alignment software, image analysis software | Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites. | software, sequence, alignment, annotation, genomic, reference, data, display, manipulation, DNA |
is related to: SEQtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust Grant 098051; NHGRI U54 HG00455 |
PMID:26801397 | Free, Available for download | SCR_015994 | SEQtools Blixem | 2026-07-28 09:44:02 | 2 |
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