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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Oct 12, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Cell Centered DatabaseResource, database, service resource, storage service resource, image repository, data repository, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented June 5, 2017. It has been merged with Cell Image Library. Database for sharing and mining cellular and subcellular high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging that makes unique and valuable datasets available to the scientific community for visualization, reuse and reanalysis. Techniques range from wide field mosaics taken with multiphoton microscopy to 3D reconstructions of cellular ultrastructure using electron tomography. Contributions from the community are welcome. The CCDB was designed around the process of reconstruction from 2D micrographs, capturing key steps in the process from experiment to analysis. The CCDB refers to the set of images taken from microscope the as the Microscopy Product. The microscopy product refers to a set of related 2D images taken by light (epifluorescence, transmitted light, confocal or multiphoton) or electron microscopy (conventional or high voltage transmission electron microscopy). These image sets may comprise a tilt series, optical section series, through focus series, serial sections, mosaics, time series or a set of survey sections taken in a single microscopy session that are not related in any systematic way. A given set of data may be more than one product, for example, it is possible for a set of images to be both a mosaic and a tilt series. The Microscopy Product ID serves as the accession number for the CCDB. All microscopy products must belong to a project and be stored along with key specimen preparation details. Each project receives a unique Project ID that groups together related microscopy products. Many of the datasets come from published literature, but publication is not a prerequisite for inclusion in the CCDB. Any datasets that are of high quality and interest to the scientific community can be included in the CCDB.electron microscope, light microscopy, electron tomography, electron microscopy, image, cell, microscopy, tomographySCR_002168(Cell Centered Database, RRID:SCR_002168)University of California at San Diego; California; USA related to: Cell Image Library (CIL), Cell Image Library (CIL), Whole Brain Catalog, Integrated Manually Extracted Annotation, used by: NIF Data Federation, Integrated Datasets, listed by: re3data.orgReferences (2)Last checked upnif-0000-00007
Information Hyperlinked Over ProteinsResource, service resource, data or information resource, databaseInformation system that provides a network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. It provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeast-two hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli.phenotype, gene, protein, interaction, pathology, physiology, gene network, network, literature, gene function, text-miningSCR_004829(Information Hyperlinked Over Proteins, RRID:SCR_004829)Autonomous University of Madrid; Madrid; Spain European Unionrelated to: PubMed, listed by: OMICtoolsPMID:15226743Last checked upnif-0000-00232, OMICS_01185
Bloomington Drosophila Stock CenterResource, organism supplier, biomaterial supply resource, service resource, storage service resource, material resource, material storage repositoryDatabase that collects, maintains and distributes Drosophila melanogaster strains for research. Emphasis is placed on genetic tools that are useful to a broad range of investigations. These include basic stocks of flies used in genetic analysis such as marker, balancer, mapping, and transposon-tagging strains; mutant alleles of identified genes, including a large set of transposable element insertion alleles; defined sets of deficiencies and a variety of other chromosomal aberrations; engineered lines for somatic and germline clonal analysis; GAL4 and UAS lines for targeted gene expression; enhancer trap and lacZ-reporter strains with defined expression patterns for marking tissues; and a collection of transposon-induced lethal mutations.disease model, deficiency, deletion, transposon insertion, sequenced strain, duplication, protein trap, human disease model, transposon, fly, gene, genetic, genetic analysis, database, deficiency, germline, insertion, invertebrate, scientist, somatic, stock, transposon, mutation, genetic constructSCR_006457(Bloomington Drosophila Stock Center, RRID:SCR_006457)Indiana University; Indiana; USA Human disease modelNIH Office of the Directorrelated to: One Mind Biospecimen Bank Listing, NIF Data Federation, used by: Integrated Animals, listed by: One Mind Biospecimen Bank ListingLast checked upnif-0000-00241https://orip.nih.gov/comparative-medicine/programs/invertebrate-modelshttp://flystocks.bio.indiana.edu/bloomhome.htm
BioGRIDResource, database, service resource, storage service resource, software resource, data repository, data or information resourceCurated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts.budding yeast, fission yeast, protein, gene, protein interaction, genetic interaction, model organism, interaction, dataset, gene annotation, phenotype, orthologous interaction, yeast, cellular interaction network, physical interaction, protein-peptide, protein-rna, protein-protein interaction, genetics, publication, raw protein, genetic interaction, web service, pathway, network, biology, gene mapping, statisticsSCR_007393(BioGRID, RRID:SCR_007393)Princeton University; New Jersey; USA , University of Edinburgh; Scotland; United Kingdom , University of Montreal; Quebec; Canada BBSRC, Canadian Institutes of Health Research, NCRR, NHGRI, NIH Office of the Directorrelated to: TissueNet - The Database of Human Tissue Protein-Protein Interactions, Pathway Commons, Cytoscape, Interaction Reference Index, ConsensusPathDB, FlyMine, IMEx - The International Molecular Exchange Consortium, Integrated Molecular Interaction Database, PSICQUIC Registry, PSI-MI, NIH Data Sharing Repositories, Agile Protein Interactomes DataServer, Integrated Manually Extracted Annotation, used by: NIF Data Federation, Monarch Initiative, recommended by: National Library of Medicine, BRAIN Initiative, listed by: re3data.org, OMICtools, DataCite, NIH Data Sharing Repositories, works_with: IMEx - The International Molecular Exchange ConsortiumReferences (4)Last checked upnif-0000-00432, OMICS_01901https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources
Gene WeaverResource, data analysis service, database, analysis service resource, production service resource, service resource, storage service resource, data repository, data or information resourceFreely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users. It was conceived of as a tool for the integration of biological functions based on the molecular processes that subserved them. From these data, an empirically derived ontology may one day be inferred. Users have found the system valuable for a wide range of applications in the arena of functional genomic data integration.phenotype, microarray, gene, genome, functional genomics, process, pathway, function, gene set, genomic data integration, analysis, visualizationSCR_003009(Gene Weaver, RRID:SCR_003009)Jackson Laboratory Integrative Neuroscience Initiative on Alcoholism, NIAAArelated to: Integrated Manually Extracted Annotation, used by: NIF Data Federation, Integrated Datasets, listed by: OMICtoolsReferences (2)Last checked upnif-0000-00517, OMICS_02232http://ontologicaldiscovery.org/
APHIDBASEResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceAphid genome database. Facilitates community annotation of pea aphid genome by International Aphid Genomics Consortium (IAGC). It aims to store recently acquired genomic resources on aphids and compare them to other insect resources as functional annotation tools. AphidBase Information System designed to organize and distribute genomic data and annotations for large international community was constructed using open source software tools from Generic Model Organism Database (GMOD).aphid, aphid gene sequence, aphid genome, aphid nervous system, genome, blast, annotate, annotation, est, functionSCR_001765(APHIDBASE, RRID:SCR_001765)INRA Rennes ANR Exdisum, ANR Genoplante, Rennes MetropoleReferences (2)Last checked downnif-0000-02554http://w3.rennes.inra.fr/AphidBasehttp://www.aphidbase.com/
BodyMap-XsResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A taxonomical and anatomical database of latest cross species animal EST data, clustered by UniGene and inter connected by Inparanoid. Users can search by Unigene, RefSeq, or Entrez Gene ID, or search for Gene Name or Tissue type. Data is also sortable and viewable based on qualities of normal, Neoplastic, or other. The last data import appears to be from 2008expressed sequence tag, comparative genomics, anatomy, taxonomy, brain, blood, connective, reproductive, muscular, alimentary, lung, liver, urinary, endocrine, exocrine, embryo, homology, gene expression, ortholog, paralogSCR_001147(BodyMap-Xs, RRID:SCR_001147)DDBJ - DNA Data Bank of Japan Neoplasm, NormalJapanese Ministry of Education Culture Sports Science and Technology MEXT, New Energy and Industrial Technology Development OrganizationReferences (3)Last checked downnif-0000-02617http://bodymap.jp/, http://bodymap.ims.u-tokyo.ac.jp/
CuticleDBResource, data or information resource, databaseA relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the five sequenced genomes where manual annotation has been applied to cuticular proteins: Anopheles gambiae, Apis mellifera, Bombyx mori, Drosophila melanogaster, and Nasonia vitripennis. Some sequences were confirmed as authentic cuticular proteins because protein sequencing revealed that they were present in cuticle; others were identified by sequence homology and other criteria. Entries provides information about whether sequences are putative or authentic cuticular proteins. CuticleDB was primarily designed to contain correct and full annotation of cuticular protein data. The database will be of help to future genome annotators. Users will be able to test hypotheses for the existence of known and also of yet unknown motifs in cuticular proteins. An analysis of motifs may contribute to understanding how proteins contribute to the physical properties of cuticle as well as to the precise nature of their interaction with chitin.genome, cuticle, cuticle protein, cuticular protein, cdna, protein, insect, exoskeleton, annotation, chitinSCR_007045(CuticleDB, RRID:SCR_007045)University of Athens Biophysics and Bioinformatics Laboratory NIAID, University of Athens; Athens; GreecePMID:15453918Last checked upnif-0000-02708
ECgene: Gene Modeling with Alternative SplicingResource, data or information resource, databaseDatabase of functional annotation for alternatively spliced genes. It uses a gene-modeling algorithm that combines the genome-based expressed sequence tag (EST) clustering and graph-theoretic transcript assembly procedures. It contains genome, mRNA, and EST sequence data, as well as a genome browser application. Organisms included in the database are human, dog, chicken, fruit fly, mouse, rhesus, rat, worm, and zebrafish. Annotation is provided for the whole transcriptome, not just the alternatively spliced genes. Several viewers and applications are provided that are useful for the analysis of the transcript structure and gene expression. The summary viewer shows the gene summary and the essence of other annotation programs. The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer. Two unique ways of analyzing gene expression is also provided. The SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publicly. The cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns.est cluster, genome, alternative splicing, splice, gene, mrna, est, annotation, gene modeling, structure, function, gene expression, transcript, genome browser, differential expression, snpSCR_007634(ECgene: Gene Modeling with Alternative Splicing, RRID:SCR_007634)Ewha Womans University; Seoul; South Korea related to: Gene Ontology, listed by: OMICtoolsReferences (3)Last checked downnif-0000-02780, OMICS_01884http://genome.ewha.ac.kr/ECgene/
EID: Exon-Intron DatabaseResource, data set, data or information resourceData sets of protein-coding intron-containing genes that contain gene information from humans, mice, rats, and other eukaryotes, as well as genes from species whose genomes have not been completely sequenced. This is a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. The database is derived from GenBank release 112, and it contains protein-coding genes that harbor introns, along with extensive descriptions of each gene and its DNA and protein sequences, as well as splice motif information. They have created subdatabases of genes whose intron positions have been experimentally determined. The collection also contains data on untranslated regions of gene sequences and intron-less genes. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames.eukaryote genome, exon, exon-intro, gene structure, genome splicing, intron, ortholog, fasta, gene, protein-coding gene, splice, motif, gene prediction, structure, coding regionSCR_002469(EID: Exon-Intron Database, RRID:SCR_002469)University of Toledo; Ohio; USA listed by: OMICtoolsReferences (2)Last checked upnif-0000-02793, OMICS_01886http://www.utoledo.edu/med/depts/bioinfo/database.htmlhttp://www.meduohio.edu/bioinfo/eid/, http://mcb.harvard.edu/gilbert/EID
Eukaryotic Promoter DatabaseResource, data or information resource, databaseDatabase for an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.promoter, polymerase, polymerase ii, promoter sequence, transcription start site, high-throughput, cage, oligocapping, chip-seq, h2az, h3k4me3, pol-ii, dna methylationSCR_002485(Eukaryotic Promoter Database, RRID:SCR_002485)SIB Swiss Institute of Bioinformatics listed by: OMICtoolsPMID:14681364Last checked upnif-0000-02806, OMICS_01880http://epd.vital-it.ch/
MIRROR: FlyBrain, An Online Atlas and Database of the Drosophila Nervous SystemResource, data processing software, training resource, software application, software resource, atlas, data or information resourceAn interactive database of the Drosophila melanogaster nervous system. It is used by the drosophila neuroscience community and by other researchers studying arthropod brain structure. Flybrain contains neuroanatomical peer reviewed descriptions of the central and peripheral nervous system of Drosophila melanogaster. It also contains an introductory hypertext tour guide to the basic structure of the nervous system, as well as more specific information concerning different anatomical structures, developmental stages, and visualization techniques for the Drosophila nervous system. Additionally, The site contains schematic representations, a 3D project, immunocytology stains, a library of golgi impregnations, and enhancer-trap images.drosophila melanogaster, drosophila melanogaster nervous system, drosophila melanogaster neuroanatomy, ganglion, gene, 3-dimensional, abdominal, anatomy, arthropod, autofluorescence, chemical, development, developmental, golgi, histology, immunocytology, impregnation, map, model, morphology, nervous system, neuroanatomical, neuroanatomy, neuron, neuropil, periphery, phenotype, structure, thoracic, visualizationSCR_007661(MIRROR: FlyBrain, An Online Atlas and Database of the Drosophila Nervous System, RRID:SCR_007661)National Institute for Basic Biology; Okazaki; Japan , University of Arizona; Arizona; USA , University of Freiburg; Baden-Wurttemberg; Germany Last checked upnif-0000-02843
GeneSpeed- A Database of Unigene Domain Organization Resource, data analysis service, resource, production service resource, analysis service resource, database, service resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Database and customized tools to study the PFAM protein domain content of the transcriptome for all expressed genes of Homo sapiens, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans tethered to both a genomics array repository database and a range of external information resources. GeneSpeed has merged information from several existing data sets including the Gene Ontology Consortium, InterPro, Pfam, Unigene, as well as micro-array datasets. GeneSpeed is a database of PFAM domain homology contained within Unigene. Because Unigene is a non-redundant dbEST database, this provides a wide encompassing overview of the domain content of the expressed transcriptome. We have structured the GeneSpeed Database to include a rich toolset allowing the investigator to study all domain homology, no matter how remote. As a result, homology cutoff score decisions are determined by the scientist, not by a computer algorithm. This quality is one of the novel defining features of the GeneSpeed database giving the user complete control of database content. In addition to a domain content toolset, GeneSpeed provides an assortment of links to external databases, a unique and manually curated Transcription Factor Classification list, as well as links to our newly evolving GeneSpeed BetaCell Database. GeneSpeed BetaCell is a micro-array depository combined with custom array analysis tools created with an emphasis around the meta analysis of developmental time series micro-array datasets and their significance in pancreatic beta cells.molecular neuroanatomy resource, drosophila melanogaster, genome, caenorhabditis elegans, c. elegans, genomics, homo sapiens, mus musculus, protein domain, transcriptomeSCR_002779( GeneSpeed- A Database of Unigene Domain Organization , RRID:SCR_002779)University of Colorado Denver; Colorado; USA NIDDKrelated to: Gene Ontology, InterPro, Pfam, UniGenePMID:17132830Last checked downnif-0000-02887http://genespeed.uchsc.edu/, http://genespeed.ccf.org
GermOnlineResource, data or information resource, databaseCross-species microarray expression database focusing on high-throughput expression data relevant for germline development, meiosis and gametogenesis as well as the mitotic cell cycle. The database contains a unique combination of information: 1) High-throughput expression data obtained with whole-genome high-density oligonucleotide microarrays (GeneChips). 2) Sample annotation (mouse over the sample name and click on it) using the Multiomics Information Management and Annotation System (MIMAS 3.0). 3) In vivo protein-DNA binding data and protein-protein interaction data (available for selected species). 4) Genome annotation information from Ensembl version 50. 5) Orthologs are identified using data from Ensembl and OMA and linked to each other via a section in the report pages. The portal provides access to the Saccharomyces Genomics Viewer (SGV) which facilitates online interpretation of complex data from experiments with high-density oligonucleotide tiling microarrays that cover the entire yeast genome. The database displays only expression data obtained with high-density oligonucleotide microarrays (GeneChips).fertility, development, germline, microarray, annotation, in vivo, protein-dna binding, protein-protein interaction, genome, ortholog, high-density oligonucleotide microarray, gene expression, genome annotation, gene orthology, genechip, tiling array, development, meiosis, gametogenesis, mitotic cell cycle, data set, data repositorySCR_002807(GermOnline, RRID:SCR_002807)National Institute of Health and Medical Research; Rennes; France bioinformatics platform of Biogenouest, National Institute of Health and Medical Research; Rennes; France, Swiss Institute of Bioinformatics, University of Rennes 1; Rennes; Francerelated to: Ensembl, OMA Browser, listed by: 3DVC, re3data.orgPMID:21149299Last checked upnif-0000-02906
HomoloGeneResource, service resource, data or information resource, databaseAutomated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase.homolog, paralog, ortholog, genome, gene, protein, protein alignment, phenotype, conserved domain, homology, amino acid sequence, cell, dna, gold standardSCR_002924(HomoloGene, RRID:SCR_002924)NCBI related to: OMIM, Mouse Genome Informatics (MGI), Zebrafish Information Network, SGD, FlyBase, ProbeMatchDB 2.0, Biomine, Consensus CDS, used by: NIF Data Federation, Nowomics, MitoMiner, listed by: OMICtools, re3data.orgPMID:23193264Last checked upnif-0000-02975, OMICS_01544http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene
HomophilaResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented on June 23, 2013. Homophila utilizes the sequence information of human disease genes from the NCBI OMIM (Online Mendelian Inheritance in Man) database in order to determine if sequence homologs of these genes exist in the current Drosophila sequence database (FlyBase). Sequences are compared using NCBI's BLAST program. The database is updated weekly and can be searched by human disease, gene name, OMIM number, title, subtitle and/or allelic variant descriptions.homolog, human disease, human disease gene, human, gene, cognateSCR_007717(Homophila, RRID:SCR_007717)University of California at San Diego; California; USA NCRRrelated to: OMIMReferences (2)Last checked upnif-0000-02976
I2DResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceDatabase of known and predicted mammalian and eukaryotic protein-protein interactions, it is designed to be both a resource for the laboratory scientist to explore known and predicted protein-protein interactions, and to facilitate bioinformatics initiatives exploring protein interaction networks. It has been built by mapping high-throughput (HTP) data between species. Thus, until experimentally verified, these interactions should be considered predictions. It remains one of the most comprehensive sources of known and predicted eukaryotic PPI. It contains 490,600 Source Interactions, 370,002 Predicted Interactions, for a total of 846,116 interactions, and continues to expand as new protein-protein interaction data becomes available.interaction, prediction, protein-protein interaction, high-throughput, model organism, mammal, eukaryote, visualization, interolog, proteinSCR_002957(I2D, RRID:SCR_002957)University of Toronto; Ontario; Canada National Science and Engineering Research Council, NIGMSrelated to: Interaction Reference Index, IMEx - The International Molecular Exchange Consortium, PSICQUIC Registry, IntActReferences (2)Last checked upnif-0000-03005
InParanoid: Eukaryotic Ortholog GroupsResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceCollection of pairwise comparisons between 100 whole genomes generated by a fully automatic method for finding orthologs and in-paralogs between TWO species. Ortholog clusters in the InParanoid are seeded with a two-way best pairwise match, after which an algorithm for adding in-paralogs is applied. The method bypasses multiple alignments and phylogenetic trees, which can be slow and error-prone steps in classical ortholog detection. Still, it robustly detects complex orthologous relationships and assigns confidence values for in-paralogs. The original data sets can be downloaded.protein, ortholog, genome, drosophila pseudoobscura, duplication, entamoeba histolytica, escherichia colik12, eukaryotic, gasterosteus aculeatus, gene, aedes aegypti, apis mellifera, bos taurus, caenorhabditis remanei, candida glabrata, canis familiaris, ciona intestinalis, cryptococcus neoformans, debaromyces hansenii, dictyostelium discoideum, genomic, homolog, inparalog, kluyveromyces lactis, macaca mulatta, monodelphis domestica, orthology, oryza sativa, outparalog, proteome, tetraodon nigroviridis, xenopus tropicalis, blast, proteome, ortholog cluster, cluster, in-paralog, paralog, automatic clustering, genome comparisonSCR_006801(InParanoid: Eukaryotic Ortholog Groups, RRID:SCR_006801)Stockholm University; Stockholm; Sweden Karolinska Institutet; Stockholm; Sweden, Pfizer Corporation, Swedish Research CouncilReferences (4)Last checked upnif-0000-03024http://www.cgb.ki.se/inparanoid/
MachiBaseResource, data or information resource, databaseDatabase for Drosophila melanogaster transcription profiling that allows users to search the Drosophilia genome, see sequence overviews, and look at various transcripts. The data were generated in conjunction with the recently developed high-throughput genome sequencer Illumina / Solexa using a newly developed 5'-end mRNA collection method. Approximately 25 million 25-27 nucleotide (nt) 5'-end mRNA tags from the embryos, larvae, young males, young females, old males, old females, and S2 (culture cell line) of D. melanogaster were collected. By arranging this vast amount of expression tag with other annotated data, they have built a one-stop service for Drosophila melanogaster transcription profiling.transcription profiling, genome, sequence, transcript, mrna, promoter, gene expression, development, embryo, larvae, young, male, female, old, s2, culture, cell line, expressed sequence tag, solexaSCR_003078(MachiBase, RRID:SCR_003078)University of Tokyo; Tokyo; Japan listed by: OMICtoolsPMID:18842623Last checked upnif-0000-03092, OMICS_01878
MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of RegulationResource, service resource, data or information resource, databaseA platform composed of three modules: the Database, the Search Engine, and rSNPs, for the computational identification of transcription factor binding sites (TFBSs) in multiple genomes, that combines TRANSFAC and JASPAR data with the search power of profile hidden Markov models (HMMs). The Database contains putative TFBSs found in the upstream sequences of genes from the human, mouse and D.melanogaster genomes. For each gene, they scanned the region from 10,000 base pairs upstream of the transcript start to 50 base pairs downstream of the coding sequence start against all their models. Therefore, the database contains putative binding sites in the gene promoter and in the initial introns and non-coding exons. Information displayed for each putative binding site includes the transcription factor name, its position (absolute on the chromosome, or relative to the gene), the score of the prediction, and the region of the gene the site belongs to. If the selected gene has homologs in any of the other two organisms, the program optionally displays the putative TFBSs in the homologs. The Search Engine allows the identification, visualization and selection of putative TFBSs occurring in the promoter or other regions of a gene from the human, mouse, D.melanogaster, C.elegans or S.cerevisiae genomes. In addition, it allows the user to upload a sequence to query and to build a model by supplying a multiple sequence alignment of binding sites for a transcription factor of interest. rSNPs MAPPER is designed to identify Single Nucleotide Polymorphisms (SNPs) that may have an effect on the presence of one or more TFBSs.transcription factor binding site, gene promoter, intron, non-coding exon, transcription factor, chromosome, gene, homolog, rsnp, single nucleotide polymorphism, search engineSCR_003077(MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of Regulation, RRID:SCR_003077)University of Florida; Florida; USA listed by: OMICtoolsReferences (2)Last checked upnif-0000-03101, OMICS_01877http://bio.chip.org/mapper
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