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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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MAIA Resource Report Resource Website 100+ mentions |
MAIA (RRID:SCR_007153) | MAIA | data analysis software, data processing software, software application, software resource | Software package of programs for complex segregation analysis in animal pedigrees. | gene, genetic, genomic, segregation, analysis, animal, pedigree |
is listed by: Genetic Analysis Software has parent organization: Institute of Cytology and Genetics of the Siberian Branch of the RAS; Novosibirsk; Russia |
Free, Non-commercial, Change of source code requires permission | nlx_154435 | SCR_007153 | 2026-09-05 06:26:07 | 359 | ||||||||
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GEISHA - Gallus Expression in Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database Resource Report Resource Website 1+ mentions |
GEISHA - Gallus Expression in Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database (RRID:SCR_007440) | GEISHA | atlas, data or information resource, data repository, database, experimental protocol, narrative resource, service resource, storage service resource | Online repository for chicken in situ hybridization information. This site presents whole mount in situ hybridization images and corresponding probe and genomic information for genes expressed in chicken embryos in Hamburger Hamilton stages 1-25 (0.5-5 days). The GEISHA project began in 1998 to investigate using high throughput whole mount in situ hybridization to identify novel, differentially expressed genes in chicken embryos. An initial expression screen of approximately 900 genes demonstrated feasibility of the approach, and also highlighted the need for a centralized repository of in situ hybridization expression data. Objectives: The goals of the GEISHA project are to obtain whole mount in situ hybridization expression information for all differentially expressed genes in the chicken embryo between HH stages 1-25, to integrate expression data with the chicken genome browsers, and to offer this information through a user-friendly graphical user interface. In situ hybridization images are obtained from three sources: 1. In house high throughput in situ hybridization screening: cDNAs obtained from several embryonic cDNA libraries or from EST repositories are screened for expression using high throughput in situ hybridization approaches. 2. Literature curation: Agreements with journals permit posting of published in situ hybridization images and related information on the GEISHA site. 3. Unpublished in situ hybridization information from other laboratories: laboratories generally publish only a small fraction of their in situ hybridization data. High quality images for which probe identity can be verified are welcome additions to GEISHA. | expression data, expression pattern, gene, gene expression, genome, chicken, chicken embryo, genomic, in situ hybridization, mapping, microarray, microrna, model organism, oligo, probe, stage, image, molecular neuroanatomy resource, embryo, embryonic chicken | has parent organization: University of Arizona; Arizona; USA | NIH ; NICHD R01HD044767 |
nif-0000-01251, r3d100012509 | https://doi.org/10.17616/R3RB6B | SCR_007440 | Gallus Expression in Situ Hybridization Analysis, GEISHA - Gallus Expression in Situ Hybridization Analysis | 2026-09-05 06:26:12 | 2 | ||||||
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Animal Genome Size Database Resource Report Resource Website 100+ mentions |
Animal Genome Size Database (RRID:SCR_007551) | Genomesize | catalog, data or information resource, data repository, database, service resource, storage service resource | Comprehensive catalogue of animal genome size data. Haploid DNA contents (C-values, in picograms) are available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources. Data may be submitted directly to the database or reprints and notifications of new papers may be sent to database curation staff. | genome size, haploid dna, non-vertebrate, vertebrate, genome structure, comparative biodiversity, sequencing, genome, genomic, FASEB list | has parent organization: University of Guelph; Ontario; Canada | Natural Sciences and Engineering Research Council of Canada | PMID:17090588 | Data taken from the database must not be reproduced in published lists, Online databases, Or other such formats, Nor redistributed without permission. The information is provided solely for personal and academic use., Please cite, The community can contribute to this resource | nif-0000-02548, r3d100012517 | https://doi.org/10.17616/R3R782, https://doi.org/10.17616/R3R782 | SCR_007551 | 2026-09-05 06:26:14 | 190 | |||||
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ALTree Resource Report Resource Website 1+ mentions |
ALTree (RRID:SCR_007562) | data analysis software, data processing software, software application, software resource | Software package to perform phylogeny based association and localization analysis.Used for association detection and localization of susceptibility sites using haplotype phylogenetic trees. Performs these two phylogeny-based analysis: tests association between candidate gene and disease; pinpoints markers (SNPs) that are putative disease susceptibility loci. | phylogeny based association, association detection, susceptibility sites, haplotype phylogenetic trees, gene, genetic, genomic |
is listed by: Genetic Analysis Software is listed by: Debian |
PMID:16595555 DOI:10.1093/bioinformatics/btl131 |
Free, Available for download, Freely available | OMICS_13032, nlx_154221 | https://sources.debian.org/src/altree/, https://gitlab.inria.fr/NGS/ALTree, | SCR_007562 | ALTREE | 2026-09-05 06:26:14 | 3 | ||||||
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MitoRes Resource Report Resource Website 1+ mentions |
MitoRes (RRID:SCR_008208) | MitoRes | data acquisition software, data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:26:19 | 1 | |||||||||
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MedBlast Resource Report Resource Website 1+ mentions |
MedBlast (RRID:SCR_008202) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. An algorithm that finds articles most relevant to a genetic sequence. In the genomic era, researchers often want to know more information about a biological sequence by retrieving its related articles. However, there is no available tool yet to achieve conveniently this goal. Here, a new literature-mining tool MedBlast is developed, which uses natural language processing techniques, to retrieve the related articles of a given sequence. An online server of this program is also provided. The genome sequencing projects generate such a large amount of data every day that many molecular biologists often encounter some sequences that they know nothing about. Literature is usually the principal resource of such information. It is relatively easy to mine the articles cited by the sequence annotation; however, it is a difficult task to retrieve those relevant articles without direct citation relationship. The related articles are those described in the given sequence (gene/protein), or its redundant sequences, or the close homologs in various species. They can be divided into two classes: direct references, which include those either cited by the sequence annotation or citing the sequence in its text; indirect references, those which contain gene symbols of the given sequence. A few additional issues make the task even more complicated: (1) symbols may have aliases; and (2) one sequence may have a couple of relatives that we want to take into account too, which include redundant (e.g. protein and gene sequences) and close homologs. Here the issues are addressed by the development of the software MedBlast, which can retrieve the related articles of the given sequence automatically. MedBlast uses BLAST to extend homology relationships, precompiled species-specific thesauruses, a useful semantics technique in natural language processing (NLP), to extend alias relationship, and EUtilities toolset to search and retrieve corresponding articles of each sequence from PubMed. MedBlast take a sequence in FASTA format as input. The program first uses BLAST to search the GenBank nucleic acid and protein non-redundant (nr) databases, to extend to those homologous and corresponding nucleic acid and protein sequences. Users can input the BLAST results directly, but it is recommended to input the result of both protein and nucleic acid nr databases. The hits with low e-values are chosen as the relatives because the low similarity hits often do not contain specific information. Very long sequences, e.g. 100k, which are usually genomic sequences, are discarded too, for they do not contain specific direct references. User can adjust these parameters to meet their own needs. | gene, article, biological, data, genome, genomic, homolog, literature, medline interfaces, mining, molecular, protein, sequence, specie | National Natural Science Foundation of China 39990600-03; Knowledge Innovation Program of the Chinese Academy of Sciences KSCX2-2-07; Knowledge Innovation Program of the Chinese Academy of Sciences KJCX1-08 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21253 | SCR_008202 | MedBlast | 2026-09-05 06:26:19 | 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) | data or information resource, database, portal, topical 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 | 2026-09-05 06:26:18 | 2 | |||||||||
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Joint Center for Structural Genomics Resource Report Resource Website 50+ mentions |
Joint Center for Structural Genomics (RRID:SCR_008251) | JCSG | institution | The JCSG is a multi-institutional consortium that aims to explore the expanding protein universe to find new challenges and opportunities to significantly contribute to new biology, chemistry and medicine through development of HT approaches to structural genomics. The mission of JCSG is to to operate a robust HT protein structure determination pipeline as a large-scale production center for PSI-2. A major goal is to ensure that innovative high-throughput approaches are developed that advance not only structural genomics, but also structural biology in general, via investigation of large numbers of high-value structures that populate protein fold and family space and by increasing the efficiency of structure determination at substantially reduced cost. The JCSG centralizes each core activity into single dedicated sites, each handling distinct, but interconnected objectives. This unique approach allows each specialized group to focus on its own area of expertise and provides well-defined interfaces among the groups. In addition, this approach addresses the requirements for the scalability needed to process large numbers of targets at a greatly reduced cost per target. JCSG production groups are: - Administrative Core - Bioinformatics Core - Crystallomics Core - Structure Determination Core - NMR Core JCSG is deeply committed to the development of new technologies that facilitate high throughput structural genomics. The areas of development include hardware, software, new experimental methods, and adaptation of existing technologies to advance genome research. In the hardware arena, their commitment is to the development of technologies that accelerate structure solution by increasing throughput rates at every stage of the production pipeline. Therefore, one major area of hardware development has been the implementation of robotics. In the software arena, they have developed enterprise resource software that track success, failures, and sample histories from target selection to PDB deposition, annotation and target management tools, and helper applications aimed at facilitating and automating multiple steps in the pipeline. Sponsors: The Joint Center for Structural Genomics is funded by the National Institute of General Medical Sciences (NIGMS), as part of the second phase of the Protein Structure Initiative (PSI) of the National Institutes of Health (U54 GM074898). | exclusion chromatography, expression, fine-structure spectroscopy, fold, absorption, affinity, bacterial, baculovirus, bioinformatics, biology, biophysical, cell, chemistry, cloning, crystallization, crystallomics, differential scanning calorimetry, diffraction, domain, genomic, gnfuge, growth, hardware, ief gel electrophoresis, macromoleuclar, medicine, microexpression, mouse, nmr, optical density, physicochemical, protein, purification, recombinatorial, robotics, sds-page, sequence, software, structural, structural biology, structure, technology, thermocycler, topoisomerase, tryptic mass spectrometry, uv/vis absorbance scan, x-ray |
has parent organization: University of California at San Diego; California; USA has parent organization: Scripps Research Institute has parent organization: Sanford Burnham Prebys Medical Discovery Institute has parent organization: Stanford University; Stanford; California |
nif-0000-22295, grid.419677.a | https://ror.org/00exr1241 | SCR_008251 | JCSG | 2026-09-05 06:26:19 | 99 | |||||||
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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, department portal, organization 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 | 2026-09-05 06:26:20 | 0 | |||||||||
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BioBank Central Resource Report Resource Website |
BioBank Central (RRID:SCR_008645) | BioBank Central | biospecimen repository, material storage repository, service resource, 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 | 2026-09-05 06:26:26 | 0 | |||||||
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Ingenuity Pathway Analysis Resource Report Resource Website 5000+ mentions Rating or validation data |
Ingenuity Pathway Analysis (RRID:SCR_008653) | IPA | pathway analysis tool | A web-based software application that enables users to analyze, integrate, and understand data derived from gene expression, microRNA, and SNP microarrays, metabolomics, proteomics, and RNA-Seq experiments, and small-scale experiments that generate gene and chemical lists. Users can search for targeted information on genes, proteins, chemicals, and drugs, and build interactive models of experimental systems. IPA allows exploration of molecular, chemical, gene, protein and miRNA interactions, creation of custom molecular pathways, and the ability to view and modify metabolic, signaling, and toxicological canonical pathways. In addition to the networks and pathways that can be created, IPA can provide multiple layering of additional information, such as drugs, disease genes, expression data, cellular functions and processes, or a researchers own genes or chemicals of interest. | software, drug, gene, analysis, chemical, metabolic, model, pathway, protein, signal, molecular signaling, genomic, pathway analysis tool |
uses: Ingenuity Pathways Knowledge Base is listed by: Biositemaps is listed by: OMICtools is listed by: SoftCite |
Commercial license | nif-0000-33144, OMICS_00399 | http://www.ingenuity.com/products/ipa, http://www.ingenuity.com/products/ipa/microrna-research | SCR_008653 | QIAGEN Ingenuity Pathway Analysis | 2026-09-05 06:26:26 | 6828 | ||||||
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genes2mind Resource Report Resource Website 1+ mentions |
genes2mind (RRID:SCR_008872) | genes2mind | analysis service resource, data analysis service, data or information resource, database, production service resource, 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 | 2026-09-05 06:26:30 | 3 | ||||||||
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Rat Genome Database (RGD) Resource Report Resource Website 100+ mentions |
Rat Genome Database (RGD) (RRID:SCR_006444) | RGD | data or information resource, data repository, database, service resource, storage service resource | Database for genetic, genomic, phenotype, and disease data generated from rat research. Centralized database that collects, manages, and distributes data generated from rat genetic and genomic research and makes these data available to scientific community. Curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data is provided. Facilitates investigators research efforts by providing tools to search, mine, and analyze this data. Strain reports include description of strain origin, disease, phenotype, genetics, immunology, behavior with links to related genes, QTLs, sub-strains, and strain sources. | RIN, Resource Information Network, mouse, rat, human, gene, qtl, marker, map, strain, sequence, est, genome, ontology, pathway, comparative genomics, physiology, phenotype, disease, model organism, proteomics, function, genetic, genomic, variation, immunology, behavior, knockout, inbred rat strain, mutant, congenic rat, recombinant inbred rat, data analysis service, organism supplier, genotype, gold standard, FASEB list, RRID Community Authority |
uses: InterMOD is used by: ChannelPedia is used by: Resource Identification Portal is used by: DisGeNET is used by: Integrated Animals is used by: NIH Heal Project is recommended by: Resource Identification Portal is listed by: re3data.org is listed by: InterMOD is listed by: Resource Information Network is affiliated with: InterMOD is related to: Rat Gene Symbol Tracker is related to: MPO is related to: NIF Data Federation is related to: MONARCH Initiative is related to: Vertebrate Trait Ontology is related to: Biositemaps is related to: One Mind Biospecimen Bank Listing is related to: AmiGO is related to: OMICtools is related to: re3data.org is related to: Integrated Manually Extracted Annotation is related to: OntoMate has parent organization: Medical College of Wisconsin; Wisconsin; USA is parent organization of: Diabetes Disease Portal is parent organization of: Rat Strain Ontology is parent organization of: Rat Strain Ontology is parent organization of: Renal Disease Portal is organization facet of: Alliance of Genome Resources |
NHLBI | PMID:23434633 PMID:18996890 PMID:17151068 |
Free, Freely available | nif-0000-00134, r3d100010417, OMICS_01660 | https://doi.org/10.17616/R3WK60 | SCR_006444 | , Rat Genome Database, RGD | 2026-09-05 06:25:53 | 280 | ||||
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PROGENY Resource Report Resource Website 100+ mentions |
PROGENY (RRID:SCR_006647) | Progeny | commercial organization, data management software, software application, software resource | Fully customizable, comprehensive genetic pedigree and clinical data management software including a multi-user relational database with an integrated pedigree drawing component to manage genetic and pedigree data in one database. Manage Pedigrees, Individuals, SNPs, STRs, Samples, Plates, Genotypes and exports to multiple analysis platforms. (entry from Genetic Analysis Software) * LIMS software, providing advanced sample tracking and management (including functionality to generate and record barcodes) and configurable workflows for your specific environment. * Full genotype management gives users the ability to track not only family-based studies, but Whole Genome Association studies containing 1000''s of samples with large arrays. | gene, genetic, genomic, c++, active x control, ms-windows, pedigree, clinical, genotype, data management, drawing, family history, questionnaire, sample, lab management, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software |
nlx_154553, OMICS_00216 | SCR_006647 | Progeny Software LLC, Progeny Software | 2026-09-05 06:25:58 | 416 | ||||||||
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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 | 2026-09-05 06:27:46 | 15 | ||||||||
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MOgene Resource Report Resource Website 50+ mentions |
MOgene (RRID:SCR_012433) | MOgene | access service resource, commercial organization, core facility, service resource | 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 | 2026-09-05 06:27:23 | 64 | |||||||
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SIFT Resource Report Resource Website 10000+ mentions |
SIFT (RRID:SCR_012813) | SIFT | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, source code, web service | 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 | 2026-09-05 06:27:27 | 10996 | |||
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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, portal, topical 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 | 2026-09-05 06:27:31 | 3 | |||||||||
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Genetic Analysis Software Resource Report Resource Website 1+ mentions |
Genetic Analysis Software (RRID:SCR_013155) | GAS | catalog, data or information resource, data set, 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 |
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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 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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 | 2026-09-05 06:27:32 | 9 | |||||
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ARP.GEE Resource Report Resource Website 1+ mentions |
ARP.GEE (RRID:SCR_013134) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application that simultaneously estimates a trait-locus position and its genetic effects for affected relative pairs (ARP) by one of two methods. Either allow a different trait-locus effect for each ARP type, or constrain the trait-locus effects according to the marginal effect of a single susceptibility locus. We include a goodness of fit statistic for the constrained model. (entry from Genetic Analysis Software) | gene, genetic, genomic, r/s-plus | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154206, SCR_009108, nlx_154232 | SCR_013134 | R/ARP.GEE | 2026-09-05 06:27:32 | 7 |
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