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http://www.fged.org/

Society that develop standards for biological research data quality, annotation and exchange. They facilitate the creation and use of software tools that build on these standards and allow researchers to annotate and share their data easily. They promote scientific discovery that is driven by genome wide and other biological research data integration and meta-analysis. Historically, FGED began with a focus on microarrays and gene expression data. However, the scope of FGED now includes data generated using any technology when applied to genome-scale studies of gene expression, binding, modification and other related applications.

Proper citation: FGED (RRID:SCR_001897) Copy   

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http://www.ncbi.nlm.nih.gov/dbSTS/

THIS RESOURCE IS NO LONGER IN SERVICE, as of October 1, 2013; however, the site is still accessible. NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites. STS sequences are incorporated into the STS Division of GenBank. The dbSTS database offers a route for submission of STS sequences to GenBank. It is designed especially for the submission of large batches of STS sequences.

Proper citation: dbSTS (RRID:SCR_000400) Copy   

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http://www.ncbi.nlm.nih.gov/ieb/research/acembly/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented August 29, 2016. AceView offers an integrated view of the human, nematode and Arabidopsis genes reconstructed by co-alignment of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes and their functions and to stimulate further validating experiments at the bench. AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals' transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated. Our goals are to offer an up-to-date resource on the genes, in the hope to stimulate further experiments at the bench, or to help medical research. AceView can be queried by meaningful words or groups of words as well as by most standard identifiers, such as gene names, Entrez Gene ID, UniGene ID, GenBank accessions.

Proper citation: AceView (RRID:SCR_002277) Copy   

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http://www.dogmap.ch/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. An international collaboration between 46 labs from 20 different countries towards a low resolution canine marker map under the auspices of the International Society for Animal Genetics (ISAG). The map under development should achieve a resolution of about 20 cM and some of the markers should be mapped physically. The participants have agreed to use microsatellites as markers on a common panel of reference families which will provide the backbone of the marker map. It is foreseen to also include type I markers in the mapping effort and to produce cosmid derived microsatellites for physical mapping. For this purpose part of the effort focuses on the standardization of the canine karyotype. Special attention is payed to hereditary diseases where efforts are under way to establish resource families either by collecting families or by specific breeding. A point of emphasis of the DogMap project is the setting up of an internationally accessible database for handling the mapping data. The structure of the DogMap collaboration includes a managing committee and scientific advisers. The managing committee is responsible for the overall coordination of the activities within the collaboration, for the dissemination of relevant information to all of the participants and for the representation of DogMap outside the collaboration., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DogMap (RRID:SCR_002332) Copy   

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http://fullmal.hgc.jp/index_ajax.html

FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum. Because of its medical importance, this organism is the first target for genome sequencing of a eukaryotic pathogen; the sequences of two of its 14 chromosomes have already been determined. However, for the full exploitation of this rapidly accumulating information, correct identification of the genes and study of their expression are essential. Using the oligo-capping method, this database has produced a full-length-enriched cDNA library from erythrocytic stage parasites and performed one-pass reading. The database consists of nucleotide sequences of 2490 random clones that include 390 (16%) known malaria genes according to BLASTN analysis of the nr-nt database in GenBank; these represent 98 genes, and the clones for 48 of these genes contain the complete protein-coding sequence (49%). On the other hand, comparisons with the complete chromosome 2 sequence revealed that 35 of 210 predicted genes are expressed, and in addition led to detection of three new gene candidates that were not previously known. In total, 19 of these 38 clones (50%) were full-length. From these observations, it is expected that the database contains approximately 1000 genes, including 500 full-length clones. It should be an invaluable resource for the development of vaccines and novel drugs. Full-malaria has been updated in at least three points. (i) 8934 sequences generated from the addition of new libraries added so that the database collection of 11,424 full-length cDNAs covers 1375 (25%) of the estimated number of the entire 5409 parasite genes. (ii) All of its full-length cDNAs and GenBank EST sequences were mapped to genomic sequences together with publicly available annotated genes and other predictions. This precisely determined the gene structures and positions of the transcriptional start sites, which are indispensable for the identification of the promoter regions. (iii) A total of 4257 cDNA sequences were newly generated from murine malaria parasites, Plasmodium yoelii yoelii. The genome/cDNA sequences were compared at both nucleotide and amino acid levels, with those of P.falciparum, and the sequence alignment for each gene is presented graphically. This part of the database serves as a versatile platform to elucidate the function(s) of malaria genes by a comparative genomic approach. It should also be noted that all of the cDNAs represented in this database are supported by physical cDNA clones, which are publicly and freely available, and should serve as indispensable resources to explore functional analyses of malaria genomes. Sponsors: This database has been constructed and maintained by a Grant-in-Aid for Publication of Scientific Research Results from the Japan Society for the Promotion of Science (JSPS). This work was also supported by a Special Coordination Funds for Promoting Science and Technology from the Science and Technology Agency of Japan (STA) and a Grant-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports and Culture of Japan.

Proper citation: Full-Malaria: Malaria Full-Length cDNA Database (RRID:SCR_002348) Copy   

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http://mrna.otago.ac.nz/

Database that provides access to mRNA sequences and associated regulatory elements that were processed from Genbank. These mRNA sequences include complete genomes, which are divided into 5-prime UTRs, 3-prime UTRs, initiation sequences, termination regions and full CDS sequences. This data can be searched for a range of properties including specific mRNA sequences, mRNA motifs, codon usage, RSCU values, information content, etc.

Proper citation: Transterm (RRID:SCR_008244) Copy   

•   Source: SciCrunch Registry

http://www.primervfx.com/#welcome

PrimerParadise is an online PCR primer database for genomics studies. The database contains predesigned PCR primers for amplification of exons, genes and SNPs of almost all sequenced genomes. Primers can be used for genome-wide projects (resequencing, mutation analysis, SNP detection etc). The primers for eukaryotic genomes have been tested with e-PCR to make sure that no alternative products will be generated. Also, all eukaryotic primers have been filtered to exclude primers that bind excessively throughout the genome. Genes are amplified as amplicons. Amplicons are defined as only one genes exons containing maximaly 3000 bp long dna segments. If gene is longer than 3000 bp then it is split into the segments at length 3000 bp. So for example gene at length 5000 bp is split into two segment and for both segments there were designed a separate primerpair. If genes exons length is over 3000 bp then it is split into amplicons as well. Every SNP has one primerpair. In addition of considering repetitive sequences and mono-dinucleotide repeats, we avoid designing primers to genome regions which contain other SNPs. -There are two ways to search for primers: you can use features IDs ( for SNP primers Reference ID, for gene/exon primers different IDs (Ensembl gene IDs, HUGO IDs for human genes, LocusLink IDs, RefSeq IDs, MIM IDs, NCBI gene names, SWISSPROT IDs for bacterial genes, VEGA gene IDs for human and mouse, Sanger S.pombe systematic gene names and common gene names, S.cerevisiae GeneBanks Locus, AccNo, GI IDs and common gene names) -you can use genome regions (chromosome coordinates, chromosome bands if exists) -Currently we provide 3 primers collections: proPCR for prokaryotic organisms genes primers -euPCR for eukaryotic organisms genes/exons primers -snpPCR for eukaryotic organisms SNP primers Sponsors: PrimerStudio is funded by the University of Tartu.

Proper citation: PrimerStudio (RRID:SCR_008232) Copy   

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http://microbialgenomics.energy.gov/index.shtml

Through its Microbial Genome Program (MGP) and its Genomics:GTL (GTL) program, DOEs Office of Biological and Environmental Research (BER) has sequenced more than 485 microbial genomes and 30 microbial communities having specialized biological capabilities. Identifying these genes will help investigators discern how gene activities in whole living systems are orchestrated to solve myriad life challenges. The MGP was begun in 1994 as a spinoff from the Human Genome Program. The goal of the program was to sequence the genomes of a number of nonpathogenic microbes that would be useful in solving DOE''s mission challenges in environmental-waste cleanup, energy production, carbon cycling, and biotechnology. Past projects include microbial genome program, microbial cell project, and the Laboratory Science Program at the DOE Joint Genome Institute. The two ongoing projects are Genomics: GTL program and Community Sequencing Program at the DOE Joint Genome Institute. Sponsors: Site sponsored by the U.S. Department of Energy Office of Science, Office of Biological and Environmental Research, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Microbial Genomics Program (RRID:SCR_008140) Copy   

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http://skonops.imbb.forth.gr/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 22, 2023. A database containing genomic/biological information on anopheline mosquitoes, with an emphasis on Anopheles gambiae, the world''''s most important malaria vector. AnoBase is an integrated, relational database of basic biological and genetic data on anopheline species, with a particular emphasis on Anopheles gambiae. It has been designed as an information source and research support tool for the broad vector biology community. Although AnoBase is not a primary genomic database that develops and provides tools to access the genome of the malaria mosquito, it nevertheless contains several sections that offer data of genomic interest such as in situ hybridization images, an integrated gene tool and direct online access to AnoXcel, the proteomic database of An. gambiae. Moreover, AnoBase also contains information on non-gambiae mosquito species and a novel section on studies related to insecticide resistance.

Proper citation: AnoBase: An Anopheles database (RRID:SCR_008166) Copy   

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http://locustdb.genomics.org.cn/

The migratory locust (Locusta migratoria) is an orthopteran pest and a representative member of hemimetabolous insects. Its transcriptomic data provide invaluable information for molecular entomology study of the insect and pave a way for comparative studies of other medically, agronomically, and ecologically relevant insects. This first transcriptomic database of the locust (LocustDB) has been developed, building necessary infrastructures to integrate, organize, and retrieve data that are either currently available or to be acquired in the future. It currently hosts 45,474 high quality EST sequences from the locust, which were assembled into 12,161 unigenes. This database contains original sequence data, including homologous/orthologous sequences, functional annotations, pathway analysis, and codon usage, based on conserved orthologous groups (COG), gene ontology (GO), protein domain (InterPro), and functional pathways (KEGG). It also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. LocustDB also provides information from comparative analysis based on data from the migratory locust and five other invertebrate species, such as the silkworm, the honeybee, the fruitfly, the mosquito and the nematode. It starts with the first transcriptome information for an orthopteran and hemimetabolous insect and will be extended to provide a framework for incorporation of in-coming genomic data of relevant insect groups and a workbench for cross-species comparative studies.

Proper citation: Migratory Locust EST Database (RRID:SCR_008201) Copy   

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http://www.ebi.ac.uk/genomes/plasmid.html

The Plasmid Genome Database aims to collate biological and genomic data for all bacterial plasmids in the hopes of enabling rapid, interrogation of both meta- and genomic data. Data maintained includes access to all plasmid genomes and information on core genomic features obtained from parsing the original EMBL/DDBJ/NCBI submission. In addition a suite of third party analyses has been performed for each genome to supplement the original annotation. This site also links to Genome Atlases provided by the Centre for Biological Sequence Analysis (CBS). The motivation behind the construction of this site derived from observations from genome sequencing projects: the abundance and inferred importance of the horizontal gene pool (HGP) in bacterial adaptation and evolution. In so far as plasmids are autonomously replicating, extrachromosomal elements they are a readily identifiable and accessible component of the HGP. Also plasmids have been identified in almost all bacterial divisions, ranging in size from less than 2 kbp to > 1.5 Mbp and as such represent a defined, yet diverse and complex sample of genes in the HGP.

Proper citation: Plasmid Genome Database (RRID:SCR_008228) Copy   

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http://alizadehlab.stanford.edu/

This is an open-source Mouse Exonic Evidence-Based Oligonucleotide Chip (MEEBOChip), and are in the process of building the human counterpart, HEEBOChip. The set of 70mers for MEEBOChip is already available from Illumina, Inc., with synthesis of HEEBOChip 70mers in progress. Both arrays are based on a novel selection of exonic long-oligonucleotides (70-mers) from a genomic annotation of the corresponding complete genome sequences, using a transcriptome-based annotation of exon structure for each genomic locus. Using a combination of existing and custom-tailored tools and datasets (including millions of mRNA and EST sequences), we built and performed a systematic examination of transcript-supported exon structure for each genomic locus at the base-pair level (i.e., exonic evidence). This strategy allowed them to select both constitutive and in many cases alternative exons for nearly every gene in the corresponding genome (e.g., protocadherin locus), allowing an unprecedented exploration of human and mouse biology. Furthermore, they used experimentally derived data to hone the selection of these 70mers, helping maximize their performance under typical fluorescent labeling and hybridization conditions. Specifically, they applied and refined the ArrayOligoSelector algorithm from Joe DeRisis laboratory to select 70mers, considering not only their uniqueness (i.e., hybridization specificity) within the content of the entire genome, but also to overcome the known biases of labeling and hybridization methods (e.g., 3-biased reverse transcription and in vitro transcription reactions).

Proper citation: Alizadehlab: MeeboChip and HeeboChip Open Source Project (RRID:SCR_008384) Copy   

•   Source: SciCrunch Registry

http://toxodb.org/toxo/

A genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, Chr Ib) strains. Sequence information is integrated with various other genomic-scale data, including community annotation, ESTs, gene expression and proteomics data. Organisms * Toxoplasma gondii (ME49, RH, GT1, Veg strains) * Neospora caninum * environmental isolate sequences from numerous species Tools * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Toxoplasma, Neospora Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * Ancillary Genome Browse: Access Additional info like Probeset data and Toxoplasma Array info

Proper citation: ApiDB ToxoDB (RRID:SCR_013453) Copy   

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http://www.informatics.jax.org/genes.shtml

Searchable database of mouse genes, DNA segments, cytogenetic markers and QTLs. MGI provides access to integrated data on mouse genes and genome features, from sequences and genomic maps to gene expression and disease models.

Proper citation: Genes, Genome Features and Maps (RRID:SCR_017524) Copy   

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http://www.genome.jp/kegg/expression/

Database for mapping gene expression profiles to pathways and genomes. Repository of microarray gene expression profile data for Synechocystis PCC6803 (syn), Bacillus subtilis (bsu), Escherichia coli W3110 (ecj), Anabaena PCC7120 (ana), and other species contributed by the Japanese research community.

Proper citation: Kyoto Encyclopedia of Genes and Genomes Expression Database (RRID:SCR_001120) Copy   

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http://www.well.ox.ac.uk/happy/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals (entry from Genetic Analysis Software) The method is implemented in a C-program and there is now an R version of HAPPY. You can run HAPPY remotely from their web server using your own data (or try it out on the data provided for download).

Proper citation: Happy (RRID:SCR_001395) Copy   

•   Source: SciCrunch Registry

http://neuronalarchitects.com/ibiofind.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. C#.NET 4.0 WPF / OWL / REST / JSON / SPARQL multi-threaded, parallel desktop application enables the construction of biomedical knowledge through PubMed, ScienceDirect, EndNote and NIH Grant repositories for tracking the work of medical researchers for ranking and recommendations. Users can crawl web sites, build latent semantic indices to generate literature searches for both Clinical Translation Science Award and non-CTSA institutions, examine publications, build Bayesian networks for neural correlates, gene to gene interactions, protein to protein interactions and as well drug treatment hypotheses. Furthermore, one can easily access potential researcher information, monitor and evolve their networks and search for possible collaborators and software tools for creating biomedical informatics products. The application is designed to work with the ModelMaker, R, Neural Maestro, Lucene, EndNote and MindGenius applications to improve the quality and quantity of medical research. iBIOFind interfaces with both eNeoTutor and ModelMaker 2013 Web Services Implementation in .NET for eNeoTutor to aid instructors to build neuroscience courses as well as rare diseases. Added: Rare Disease Explorer: The Visualization of Rare Disease, Gene and Protein Networks application module. Cinematics for the Image Finder from Yale. The ability to automatically generate and update websites for rare diseases. Cytoscape integration for the construction and visualization of pathways for Molecular targets of Model Organisms. Productivity metrics for medical researchers in rare diseases. iBIOFind 2013 database now includes over 150 medical schools in the US along with Clinical Translational Science Award Institutions for the generation of biomedical knowledge, biomedical informatics and Researcher Profiles.

Proper citation: iBIOFind (RRID:SCR_001587) Copy   

•   Source: SciCrunch Registry

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http://www.nitrc.org/projects/plink

Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software.

Proper citation: PLINK (RRID:SCR_001757) Copy   

•   Source: SciCrunch Registry

https://www.snpstats.net/

A web-based application designed from a genetic epidemiology point of view to analyze association studies using single nucleotide polymorphisms (SNPs). For each selected SNP, you will receive: * Allele and genotype frequencies * Test for Hardy-Weinberg equilibrium * Analysis of association with a response variable based on linear or logistic regression * Multiple inheritance models: co-dominant, dominant, recessive, over-dominant and additive * Analysis of interactions (gene-gene or gene-environment) If multiple SNPs are selected: * Linkage disequilibrium statistics * Haplotype frequency estimation * Analysis of association of haplotypes with the response * Analysis of interactions (haplotypes-covariate)

Proper citation: SNPSTATS (RRID:SCR_002142) Copy   

•   Source: SciCrunch Registry

http://www.aspgd.org/

Database of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input sequence. *Find similarities between a sequence of interest and fungal nucleotide or protein sequences. AspGD welcomes data submissions.

Proper citation: ASPGD (RRID:SCR_002047) Copy   

•   Source: SciCrunch Registry