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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Zebrafish Genome Project Resource Report Resource Website 50+ mentions |
Zebrafish Genome Project (RRID:SCR_013157) | database, data or information resource | Database of zebrafish genome. | Zebrafish, genome |
is related to: Genome Reference Consortium is related to: Zebrafish Information Network (ZFIN) has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Free, Freely available | SCR_017503, nif-0000-31931 | https://www.sanger.ac.uk/science/data/zebrafish-genome-project | SCR_013157 | Danio rerio Sequencing Project | 2026-08-04 09:43:09 | 67 | |||||||
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Fugu Genome Project Resource Report Resource Website 10+ mentions |
Fugu Genome Project (RRID:SCR_013014) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE,documented on August 16, 2019. Fugu genome is among the smallest vertebrate genomes and has proved to be a valuable reference genome for identifying genes and other functional elements such as regulatory elements in the human and other vertebrate genomes, and for understanding the structure and evolution of vertebrate genomes. This site presents version 4 of the Fugu genome, released in October 2004 by the International Fugu Genome Consortium. Fugu rubripes has a very compact genome, with less than 15 consisting of dispersed repetitive sequence, which makes it ideal for gene discovery. A draft sequence of the fugu genome was determined by the International Fugu Genome Consortium in 2002 using the ''whole-genome shotgun'' sequencing strategy. Fugu is the second vertebrate genome to be sequenced, the first being the human genome. This webpage presents the annotation made on the fourth assembly by the IMCB team using the Ensembl annotation pipeline. We are continuing with the gap filling work and linking of the scaffolds to obtain super-contigs. | element, evolution, fish, fugu, functional, gene, genome, human, pufferfish, regulatory, rubripes, structure, vertebrate, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Institute of Molecular and Cell Biology; Singapore; Singapore |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fugu-sg, nif-0000-20988 | https://bio.tools/fugu-sg | SCR_013014 | FGP | 2026-08-04 09:43:07 | 22 | |||||||
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Cerebellar Development Transcriptome Database Resource Report Resource Website 1+ mentions |
Cerebellar Development Transcriptome Database (RRID:SCR_013096) | CDT-DB | atlas, database, data or information resource | Transcriptomic information (spatiotemporal gene expression profile data) on the postnatal cerebellar development of mice (C57B/6J & ICR). It is a tool for mining cerebellar genes and gene expression, and provides a portal to relevant bioinformatics links. The mouse cerebellar circuit develops through a series of cellular and morphological events, including neuronal proliferation and migration, axonogenesis, dendritogenesis, and synaptogenesis, all within three weeks after birth, and each event is controlled by a specific gene group whose expression profile must be encoded in the genome. To elucidate the genetic basis of cerebellar circuit development, CDT-DB analyzes spatiotemporal gene expression by using in situ hybridization (ISH) for cellular resolution and by using fluorescence differential display and microarrays (GeneChip) for developmental time series resolution. The CDT-DB not only provides a cross-search function for large amounts of experimental data (ISH brain images, GeneChip graph, RT-PCR gel images), but also includes a portal function by which all registered genes have been provided with hyperlinks to websites of many relevant bioinformatics regarding gene ontology, genome, proteins, pathways, cell functions, and publications. Thus, the CDT-DB is a useful tool for mining potentially important genes based on characteristic expression profiles in particular cell types or during a particular time window in developing mouse brains. | gene expression, fluorescence, function, gene, gene chip, genome, bioinformatics, brain, cell, cerebellum, development, in situ hybridization, fluroescence differential display, cerebellar development, microarray, mining, mouse, mrna, ontology, pathway, protein, rt-pcr, molecular neuroanatomy resource, transcriptiome, spatiotemporal, cdna microarray, genechip, postnatal, histochemistry, image, postnatal development |
is related to: Gene Ontology is related to: RIKEN integrated database of mammals has parent organization: RIKEN Brain Science Institute |
Brain development, Brain disorder | INCF Japan Node ; Japan Society for the Promotion of Science ; Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Japan Science and Technology Agency |
PMID:18603407 | To be used for research and educational purposes only. Any reproduction or use for commercial purposes is prohibited without the prior express written permission of the RIKEN. | nif-0000-00008 | SCR_013096 | 2026-08-04 09:43:08 | 1 | |||||
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Comparative Genometrics Resource Report Resource Website |
Comparative Genometrics (RRID:SCR_012920) | database, data or information resource | The Comparative Genometrics website displays for sequenced genomes, three different genometric analyses: the DNA walk and the GC and TA skews during the initial phase. Although primarily focused on prokaryotic chromosomes, the CG website posts genometric information on paradigm plasmids, phages, viruses, and organelles. The genometric analyses are available via phylogenetic tree or alphabetical list. It also offers small genome information, for mitochondria, chloroplasts, viruses, bacteriophages, and plasmids. | genome, bacteriophages, chloroplasts, genometric analyses, mitochondria, phage, plasmids, prokaryotic chromosome, sequenced genome, viruses | has parent organization: University of Lausanne; Lausanne; Switzerland | nif-0000-02682 | SCR_012920 | Comparative Genometrics | 2026-08-04 09:43:06 | 0 | |||||||||
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doRiNA Resource Report Resource Website 10+ mentions |
doRiNA (RRID:SCR_013222) | doRiNA | database, data or information resource | In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. For computational miRNA target site predictions, we provide an update of PicTar predictions. | binding site, rna binding protein, microrna, post-transcription, rna, gene, genome, mammal, population variation, gene expression, transcript, regulator, protein, binding |
is related to: UCSC Genome Browser has parent organization: Max Delbruck Center for Molecular Medicine; Berlin; Germany |
MDC Systems Biology Network ; BMBF ; Senate of Berlin; Berlin; Germany ; DFG |
PMID:22086949 | nlx_151321, r3d100011087 | SCR_013222 | 2026-08-04 09:43:10 | 15 | |||||||
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Drosophila melanogaster Exon Database Resource Report Resource Website 1+ mentions |
Drosophila melanogaster Exon Database (RRID:SCR_013441) | DEDB | database, data or information resource | Database on Drosophila melanogaster exons presented in a splicing graph form. Data is based on release 3.2 of the Drosophila melanogaster genome annotations available at FlyBase. The gene structure information extracted from the annotations were checked, clustered and transformed into splicing graph. The splicing graph form of the gene constructs were then used for classification of the various types of alternative splicing events. In addition, Pfam domains were mapped onto the gene structure. Users can query the database using the query page using BLAST, FlyBase Gene Name, FlyBase Gene Symbol, Pfam Accession Number and Pfam Identifier. This allows users to determine the Drosophila melanogaster homology of their gene using a BLAST search and to visualize the alternative splicing variants if any. Users can also determine genes containing a particular domain using the Pfam Accession Numbers and Identifiers. | exon, gene, alternative splicing, annotation, classification, cluster, domain, genome, graph, homology, protein, splicing, structure, transcript, visualize, blast |
is listed by: OMICtools is related to: FlyBase has parent organization: National University of Singapore; Singapore; Singapore |
Agency for Science Technology and Research | PMID:15581431 | nif-0000-21118, OMICS_01894 | SCR_013441 | DEDB - Drosophila melanogaster Exon Database, DEDB : Drosophila melanogaster Exon Database | 2026-08-04 09:43:13 | 2 | ||||||
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ApiDB ToxoDB Resource Report Resource Website 100+ mentions |
ApiDB ToxoDB (RRID:SCR_013453) | ApiDB ToxoDB | database, data or information resource | 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 | end-sequencing, bac clone, data mining tool, microarray, proteomic sequencing, toxoplasma gondii, bac clone, 8x random shotgun, genomic sequencing project, snp, qtl, sequencing, genomic, non-vertebrate, unicellular, eukaryote, genome, pathogen, toxoplasmosis, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Eukaryotic Pathogen Database Resources |
NIAID contract HHSN266200400037C | PMID:18003657 PMID:12519989 |
r3d100012266, nif-0000-03572, biotools:toxodb | https://bio.tools/toxodb | http://ToxoDB.org | SCR_013453 | Toxoplasma Genomics Resource, ToxoDB | 2026-08-04 09:43:13 | 137 | ||||
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Tree families database Resource Report Resource Website 50+ mentions |
Tree families database (RRID:SCR_013401) | database, data or information resource | A database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families. TreeFam defines a gene family as a group of genes that evolved after the speciation of single-metazoan animals. It also tries to include outgroup genes like yeast (S. cerevisiae and S. pombe) and plant (A. thaliana) to reveal these distant members.TreeFam is also an ortholog database. Unlike other pairwise alignment based ones, TreeFam infers orthologs by means of gene trees. It fits a gene tree into the universal species tree and finds historical duplications, speciations and losses events. TreeFam uses this information to evaluate tree building, guide manual curation, and infer complex ortholog and paralog relations.The basic elements of TreeFam are gene families that can be divided into two parts: TreeFam-A and TreeFam-B families. TreeFam-B families are automatically created. They might contain errors given complex phylogenies. TreeFam-A families are manually curated from TreeFam-B ones. Family names and node names are assigned at the same time. The ultimate goal of TreeFam is to present a curated resource for all the families. phylogenetic tree, animal, vertebrate, invertebrate, gene, ortholog, paralog, evolutionary history, gene families, single-metazoan animals, outgroup genes like yeast (S. cerevisiae and S. pombe), plant (A. thaliana), historical duplications, speciations, losses, Human, Genome, comparative genomics | evolutionary history, gene, gene families, genome, animal, comparative genomics, historical duplications, human, invertebrate, losses, ortholog, outgroup genes like yeast (s. cerevisiae and s. pombe), paralog, phylogenetic tree, plant (a. thaliana), single-metazoan animals, speciations, vertebrate, FASEB list |
is related to: FlyMine has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
nif-0000-03588 | SCR_013401 | Tree families database, TreeFam | 2026-08-04 09:43:12 | 85 | |||||||||
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EchinoBase Resource Report Resource Website 100+ mentions |
EchinoBase (RRID:SCR_013732) | database, data or information resource | Database that provide a genomic information and comparative genomics platform on sea urchins and related echinoderms. It provide collection of information to directly support experimental work on these useful research models in cell and developmental biology. | sea urchins, echinoderms, genome, FASEB list | NIH Office of the Director P40 OD010959 | PMID:19010966 | Free, Public | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources | SCR_013732 | SpBase, Echinoderm genomic database, Gene Library Resource for the Sea Urchin Strongylocentrotus purpuratus, Sea Urchin Genome Database, Echino Base | 2026-08-04 09:43:16 | 104 | |||||||
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Kazusa Arabidopsis data opening site Resource Report Resource Website 1+ mentions |
Kazusa Arabidopsis data opening site (RRID:SCR_013511) | database, data or information resource | This site has been developed by Kazusa DNA Research Institute for the purpose of offering the science community the analyzed sequence data produced by a multi-national Arabidopsis genome sequencing project coordinated by the Arabidopsis Genome Initiatives (AGI). The aim of this service is to enable users to browse the annotated sequence data produced by all the sequencing teams of AGI through an user-friendly graphic display system and search engines. Gene structures proposed on the annotated sequences as well as those predicted by computer programs are presented and each graphic item has a hyperlink to detailed information of the corresponding area. The nucleotide sequence data deposited in GenBank by AGI was downloaded, re-computer-analyzed at Kazusa and parsed results are displayed graphically. | annoated, arabidopsis, dna, genome, sequence | nif-0000-20958 | SCR_013511 | KAOS | 2026-08-04 09:43:14 | 6 | ||||||||||
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Genes, Genome Features and Maps Resource Report Resource Website 1+ mentions |
Genes, Genome Features and Maps (RRID:SCR_017524) | database, data or information resource | 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. | Data, mouse, gene, DNA, segment, cytogenetic, marker, MGI, genome, feature, sequenced, genomic, map, expression, disease, model | Free, Freely available | SCR_017524 | 2026-08-04 09:44:09 | 5 | |||||||||||
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miRanda Resource Report Resource Website 100+ mentions |
miRanda (RRID:SCR_017496) | database, data or information resource, service resource | Comprehensive resource of microRNA target predictions and expression profiles. Used for whole genome prediction of miRNA target genes. For each miRNA, target genes are selected on basis of sequence complementarity using position weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Provides information about set of genes potentially regulated by particular microRNA, co-occurrence of predicted target sites for multiple microRNAs in mRNA and microRNA expression profiles in tissues. Users are allowed to customize algorithm, numerical parameters, and position-specific rules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Whole, genome, prediction, miRNA, target, gene, expression, profile, data, FASEB list | is listed by: SoftCite | NIGMS ; Atlantic Philanthropies ; Alfred W. Bressler Scholars Endowment Fund |
PMID:18158296 | THIS RESOURCE IS NO LONGER IN SERVICE | http://www.microrna.org/microrna/home.do | SCR_017496 | MicroRNA.org. microrna.org | 2026-08-04 09:44:09 | 210 | ||||||
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mqtldb Resource Report Resource Website 10+ mentions |
mqtldb (RRID:SCR_018002) | mqtldb | database, data or information resource | Data collection of large scale genome wide DNA methylation analysis of 1,000 mother-child pairs at serial time points across life course (ARIES). | Data, large scale, genome, DNA methylation, analysis, mother-child pair, serial time point, life course, aeries, methylation, quantitative trait loci, database | DOI:10.1186/s13059-016-0926-z | SCR_018002 | methylation quantitative trait loci database | 2026-08-04 09:44:15 | 36 | |||||||||
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LAMHDI: The Initiative to Link Animal Models to Human DIsease Resource Report Resource Website 1+ mentions |
LAMHDI: The Initiative to Link Animal Models to Human DIsease (RRID:SCR_008643) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, it has been replaced by Monarch Initiative. LAMHDI, the initiative to Link Animal Models to Human DIsease, is designed to accelerate the research process by providing biomedical researchers with a simple, comprehensive Web-based resource to find the best animal model for their research. LAMDHI is a free, Web-based, resource to help researchers bridge the gap between bench testing and human trials. It provides a free, unbiased resource that enables scientists to quickly find the best animal models for their research studies. LAMHDI includes mouse data from MGI, the Mouse Genome Informatics website; zebrafish data from ZFIN, the Zebrafish Model Organism Database; rat data from RGD, the Rat Genome Database; yeast data from SGD, the Saccharomyces Genome Database; and fly data from FlyBase. LAMHDI.org is operational today, and data is added regularly. Enhancements are planned to let researchers contribute their knowledge of the animal models available through LAMHDI. The LAMHDI goal is to allow researchers to share information about and access to animal models so they can refine research and testing, and reduce or replace the use of animal models where possible. LAMHDI Database Search: LAMHDI brings together scientifically validated information from various sources to create a composite multi-species database of animal models of human disease. To do this, the LAMHDI database is prepared from a variety of sources. The LAMHDI team takes publicly available data from OMIM, NCBI''s Entrez Gene database, Homologene, and WikiPathways, and builds a mathematical graph (think of it as a map or a web) that links these data together. OMIM is used to link human diseases with specific human genes, and Entrez provides universal identifiers for each of those genes. Human genes are linked to their counterpart genes in other species with Homologene, and those genes are linked to other genes tentatively or authoritatively using the data in WikiPathways. This preparatory work gives LAMHDI a web of human diseases linked to specific human genes, orthologous human genes, homologous genes in other species, and both human and non-human genes involved in specific metabolic pathways associated with those diseases. LAMHDI includes model data that partners provide directly from their data structures. For instance, MGI provides information about mouse models, including a disease for each model, as well as some genetic information (the ID of the model, in fact, identifies one or more genes). ZFIN provides genetic information for each zebrafish model, but no diseases, so zebrafish models are integrated by using the genes as the glue. For instance, a zebrafish model built to feature the zebrafish PKD2 gene would plug into the larger disease-gene map at the node representing the zebrafish PKD2 gene, which is connected to the node representing the human PKD2 gene, which in turn is connected to the node representing the human disease known as polycystic kidney disease. (Some of the partner data LAMHDI receives can even extend the base map. MGI provides a disease for every model, and in some cases this allows the creation of a disease-to-gene relationship in the LAMHDI database that might not already be documented in the OMIM dataset.) With curatorial and model information in hand, LAMHDI runs a lengthy automated process that exhaustively searches for every possible path between each model and each disease in the data, up to a set number of hops, producing for each disease-to-model pair a set of links from the disease to the model. The algorithm avoids circular paths and paths that include more than one disease anywhere in the middle of the path. At the end of this phase, LAMHDI has a comprehensive set of paths representing all the disease-to-model relationships in the data, varying in length from one hop to many hops. Each disease-to-model path is essentially a string of nodes in the data, where each node represents a disease, a gene, a linkage between genes (an orthologue, a homologue, or a pathway connection, referred to as a gene cluster or association), or a model. Each node has a human-friendly label, a set of terms and keywords, and - in most cases - a URL linking the node to the data source where it originated. When a researcher submits a search on the LAMHDI website, LAMHDI searches for the user''s search terms in its precomputed list of all known disease-to-model paths. It looks for the terms not only in the disease and model nodes, but also in every node along each path. The complete set of hits may include multiple paths between any given disease-to-model pair of endpoints. Each of these disease-to-model pair sets is ordered by the number of hops it involves, and the one involving the fewest hops is chosen to represent its respective disease-to-model pair in the search results presented to the user. Results are sorted by scores that represent their matches. The number of hops is one barometer of the strength of the evidence linking the model and the disease; fewer hops indicates the relationship is stronger, more hops indicates it may be weaker. This indicator works best for comparing models from a single partner dataset: MGI explicitly identifies a disease for each mouse model, so there can be disease-to-model hits for mice that involve just one hop. Because ZFIN does not explicitly identify a disease for each model, no zebrafish model will involve fewer than four hops to the nearest disease, from the zebrafish model to a zebrafish gene to a gene cluster to a human gene to a human disease. | fly, animal, biologic, community, database, disease, genome, human, informatics, international, internet, knockout, model, mouse, network, organism, pathway, primate, rat, research, saccharomyces, testing, treatment, trial, worm, zebrafish |
has parent organization: University of Washington; Seattle; USA has parent organization: University of Wisconsin-Madison; Wisconsin; USA has parent organization: University of California at San Diego; California; USA |
NIH OD011883; NIH NS058296 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-32417 | SCR_008643 | LAMHDI | 2026-08-04 09:42:11 | 2 | |||||||
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Transterm Resource Report Resource Website 10+ mentions |
Transterm (RRID:SCR_008244) | database, data or information resource | 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. | element, gene, 3' utr, 5' utr, codon, genome, genomic, initiation, motif, mrna, nucleotide sequences, transcriptional regulator sites, transcription factors databases, region, regulatory, rna sequence, species, termination |
is listed by: Debian is listed by: OMICtools has parent organization: University of Otago; Dunedin; New Zealand |
DOI:10.1186/gb-2007-8-2-r22 | Public | nif-0000-21399, OMICS_06165 | https://sources.debian.org/src/transtermhp/ | http://uther.otago.ac.nz/Transterm.html | SCR_008244 | 2026-08-04 09:42:07 | 17 | ||||||
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PrimerStudio Resource Report Resource Website 1+ mentions |
PrimerStudio (RRID:SCR_008232) | database, data or information resource | 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. | eukaryotic, exon, gene, amplicon, amplifcation, analysis, dinucleotide, dna, genome, genomic, molecular probe and primer databases, mononucleotide, mutation, organism, pcr, primer, prokaryotic, region, repetitive, segment, sequence, snp, snp detection | nif-0000-21334 | SCR_008232 | PrimerStudio | 2026-08-04 09:42:07 | 1 | ||||||||||
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Mammalian Protein Complex Data Base Resource Report Resource Website |
Mammalian Protein Complex Data Base (RRID:SCR_008209) | database, data or information resource | A database of manually annotated mammalian protein complexes. To obtain a high-quality dataset, information was extracted from individual experiments described in the scientific literature. Data from high-throughput experiments was not included. | gene, genome, mammalian, protein, proteomics, structure | The Munich Information Center for Protein Sequences ; MPCDB |
nif-0000-21273 | SCR_008209 | 2026-08-04 09:42:04 | 0 | ||||||||||
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Alzheimer Disease and Frontotemporal Dementia Mutation Database Resource Report Resource Website 1+ mentions |
Alzheimer Disease and Frontotemporal Dementia Mutation Database (RRID:SCR_008286) | database, data or information resource | A locus-specific database aimed at collecting known mutations and non-pathogenic coding variations in the genes related to Alzheimer disease (AD) and frontotemporal dementia (FTD), following the guidelines of the Human Genome Variation Society. Mutations can be retrieved based on the gene, phenotype and publication. The database contains mutations reported in the literature and at scientific meetings, and unpublished mutations directly submitted to the database. To date, AD&FTDMDB contains mutations in the genes encoding the Amyloid Beta Precursor Protein (APP), Presenilin 1 (PSEN1), Presenilin 2 (PSEN2), Chromatin Modifying Protein 2B (CHMP2B), fusion (involved in t(12;16) in malignant liposarcoma) (FUS), Granulin (GRN), Microtubule Associated Protein Tau (MAPT), TAR DNA binding protein (TARDBP) and Valosin-containing Protein (VCP) and holds 415 different mutations observed in 1027 patients or families. As of March 2013, the latest publications referenced were from 2008, indicating that this resource may not be up to date. | frontotemporal dementia, gene, alzheimers disease, genome, mrna, mutation, phenotype, single nucleotide polymorphism | has parent organization: University of Antwerp; Antwerp; Belgium | Alzheimer's disease, Frontotemporal dementia | PMID:17392794 | r3d100012441, nif-0000-23934 | https://doi.org/10.17616/R3277G, https://doi.org/10.17616/R3277G | SCR_008286 | ADandFTDMDB, AD and FTD Mutation Database | 2026-08-04 09:42:06 | 7 | ||||||
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Plasmid Genome Database Resource Report Resource Website 10+ mentions |
Plasmid Genome Database (RRID:SCR_008228) | database, data or information resource | 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. | element, evolution, extrachromosomal, gene, adaptation, atlas, autonomous, bacterial, biological, division, genome, genomic, hgp, plasmid, pool, prokaryote databases, replicate | nif-0000-21323 | http://www.genomics.ceh.ac.uk/plasmiddb/ | SCR_008228 | PGD | 2026-08-04 09:42:04 | 21 | |||||||||
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Protochlamydia amoebophila UWE25 Resource Report Resource Website |
Protochlamydia amoebophila UWE25 (RRID:SCR_008222) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. This is the official database of the environmental chlamydia genome project. This resource provides access to finished sequence for Parachlamydia-related symbiont UWE25 and to a wide range of manual annotations, automatical analyses and derived datasets. Functional classification and description has been manually annotated according to the Annotation guidelines. Chlamydiae are the major cause of preventable blindness and sexually transmitted disease. Genome analysis of a chlamydia-related symbiont of free-living amoebae revealed that it is twice as large as any of the pathogenic chlamydiae and had few signs of recent lateral gene acquisition. We showed that about 700 million years ago the last common ancestor of pathogenic and symbiotic chlamydiae was already adapted to intracellular survival in early eukaryotes and contained many virulence factors found in modern pathogenic chlamydiae, including a type III secretion system. Ancient chlamydiae appear to be the originators of mechanisms for the exploitation of eukaryotic cells. Environmental chlamydiae have recently been recognized as obligate endosymbionts of free-living amoebae and have been implicated as potential human pathogens. Environmental chlamydiae form a deep branching evolutionary lineage within the medically important order Chlamydiales. Despite their high diversity and ubiquitous distribution in clinical and environmental samples only limited information about genetics and ecology of these microorganisms is available. The Parachlamydia-related Acanthamoeba symbiont UWE25 was therefore selected as representative environmental chlamydia strain for whole genome sequencing. Comparative genome analysis was performed using PEDANT and simap. Sponsors: The environmental chlamydia genome project was funded by the bmb+f (German Federal Ministry of Education and Research) and is part of the Competence Network PathoGenoMiK. | ecology, endosymbiont, environmental, eukaryote, eukaryotic, evolutionary, functional, gene, genetic, acanthamoeba, amoebae, blindness, cell, chlamydia, classification, clinical, genome, human, intracellular, lateral, lineage, mechanism, microorganism, obligate, parachlamydia, pathogen, pathogenic, sequence, sexually, strain, survival, symbiont, transmitted disease, uwe25, virulence | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21310 | SCR_008222 | Protochlamydia amoebophila UWE25 | 2026-08-04 09:42:04 | 0 |
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