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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: Sep 14, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
cpnDB: A Chaperonin DatabaseResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceA curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences.chaperonin sequence, microbial ecology, phylogenetics, chaperonin, plastid, mitochondria, cytoplasm, sequence, blast, fastaSCR_002263(cpnDB: A Chaperonin Database, RRID:SCR_002263)Canadian Biotechnology Strategy, National Research Council Genomics and Health Initiativelisted by: OMICtoolsPMID:15289485Last checked downnif-0000-02694, OMICS_01511http://cpndb.cbr.nrc.ca/
Tribolium castaneum Genome ProjectResource, topical portal, data or information resource, portal, databaseThis portal provides information about the Tribolium castabeum Genome Project. The Tribolium castaneum genome sequence and its analysis has been published in Nature, two companion journal issues (IBMB and DGE) and numerous other publications listed below. The red flour beetle, Tribolium castaneum, a common pest that is also a genetic model for the Coleoptera. The genome has been sequenced to 7-fold coverage using a whole genome shotgun approach and assembled using the HGSC's assembly engine, Atlas, with methods employed for the Drosophila pseudoobscura genome assembly. Approximately 90% of the genome sequence has been mapped to chromosomes in collaboration with Dick Beeman (USDA ARS) and Sue Brown (Kansas State University). Access to the Data :- Genome Assembly: The long term home of the Tribolium genome is Beetlebase. Tcas 3.0 is now available in GenBank and on our FTP site. Note there are no restrictions of any kind on the Tribolium data as it has been published. Version 2 of the assembly, Tcas_2.0 is available for download using the FTP Data link in the sidebar. The assembly is described in detail in the README in that directory. T.cas_1.0 was a preliminary genome assembly that did not include large insert paired end information and has been moved to a previous assemblies folder. A genboree browser of the Tcas2.0 sequence is available here: There are also links to the genboree browser from the blast results (at the bottom of each reported HSP) if you use the blast server on this page. The original linear scaffold file, Tcas2.0/linearScaffolds/Tcas20050914-genome, posted on the ftp site did not include singleton contigs from the assembly and thus did not fully reflect the tribolium genome sequence, missing ~4.4Mb of sequence in 1860 contigs and reptigs or approximately 2.5% of the assembled sequence. A corrected Tcas20051011-genome file containing these missing sequences is now available on the ftp site. The blast databases have also been updated to reflect this change. All other data is correct, and not affected by this change. :- BLAST Searches: The BLAST link is located in the sidebar. :* Linearized chromosome and unplaced scaffold sequences :* Assembled contigs :* Bin0 unassembled reads and Repeat reads Traces are available from the NCBI Trace Archive by using the link in the sidebar, or by using NCBI MegaBLAST with a same species or cross species query. Sponsors: Funding for this project has been provided by the National Human Genome Research Institute (NHGRI U54 HG003273), which is part of the National Institutes of Health (NIH), and the U.S. Department of Agriculture's Agricultural Research Service (USDA ARS Agreement No. 58-5430-3-338).genetic, chromosome, coleoptera, drosophila, genome, model, pest, red flour beetle, sequence, tribolium castaneumSCR_002848(Tribolium castaneum Genome Project, RRID:SCR_002848)Baylor University; Texas; USA Last checked downnif-0000-25607http://www.hgsc.bcm.tmc.edu/project-species-i-Tribolium%20castaneum.hgsc?pageLocation=Tribolium%20castaneum
Tuschl Laboratory: RNA Molecular BiologyResource, laboratory portal, portal, organization portal, data or information resourceRNA is not only a carrier of genetic information, but also a catalyst and a guide for sequence-specific recognition and processing of other RNA molecules. This lab investigates the regulatory mechanisms of RNA interference, RNA-mediated translational control, and nuclear pre-mRNA splicing. Classical and combinatorial biochemical techniques are used to analyze the function of the RNA- and protein-components involved in those processes.genetics, biochemical, biology, catalyst, mechanism, mirna, molecule, process., protein, regulation, rna, sequence, sirna, techniqueSCR_002866(Tuschl Laboratory: RNA Molecular Biology, RRID:SCR_002866)Rockefeller University; New York; USA Last checked downnif-0000-25546http://www.rockefeller.edu/labheads/tuschl/sirna.html
Honey Bee Genome ProjectResource, topical portal, portal, data or information resourceThe HGSC has sequenced the honey bee, Apis mellifera. The version 4.0 assembly was released in March 2006 and published in October 2006. The genome sequence is being upgraded with additional sequence coverage. The honey bee is important in the agricultural community as a producer of honey and as a facilitator of pollination. It is a model organism for studying the following human health issues: immunity, allergic reaction, antibiotic resistance, development, mental health, longevity and diseases of the X chromosome. In addition, biologists are interested in the honey bee's social organization and behavioral traits. This project was proposed to the HGSC by a group of dedicated insect biologists, headed by Gene Robinson. Following a workshop at the HGSC and a honey bee white paper, the HGSC began the project in 2002. A 6-fold coverage WGS, BAC sequence from pooled arrays, and an initial genome assembly (Amel_v1.0) were released beginning in 2003. This has been a challenging project with difficulty in recovering AT-rich regions. The WGS data had lower coverage in AT-rich regions and BAC data from clones showed evidence of internal deletions. Additional reads from AT enriched DNA addressed these underrepresented regions. The current assembly Amel_4.0 was produced with Atlas and includes 2.7 million reads (1.8 Gb) or 7.5x coverage of the (clonable) genome. About 97% of STSs, 98% of ESTs, and 96% of cDNAs are represented in the 231 Mb assembly. About 2,500 reads were also produced from a strain of Africanized honey bee and SNPs were extracted. These were released in dbSNP and the NCBI Trace Archive. Analysis of the genome by a consortium of 20 labs has been completed. This produced a gene list derived from five different methods melded through the GLEAN software. Publications include a main paper in Nature and up to forty companion papers in Genome Research and Insect Molecular Biology. Sponsors: Sequencing of the honey bee is jointly funded by National Human Genome Research Institute (NHGRI) and the Department of Agriculture (USDA). Multiple drones from the same queen (strain DH4) were obtained from Danny Weaver of B. Weaver Apiaries. All libraries were made from DNA isolated from these drones. The honey bee BAC library (CHORI-224) was prepared by Pieter de Jong and Katzutoyo Osoegawa at the Children's Hospital Oakland Research Institute.gene, agricultural, allergy, antibiotic, apis mellifera, array, behavioral, biologist, chromosome, development, disease, genome, heath, honey bee, human, immunity, insect, mental heath, organism, pollination, reaction, resistance, sequence, traitSCR_002890(Honey Bee Genome Project, RRID:SCR_002890)Baylor University; Texas; USA Last checked downnif-0000-25604http://www.hgsc.bcm.tmc.edu/project-species-i-Apis%20mellifera.hgsc?pageLocation=Apis%20mellifera
ISFinderResource, data analysis service, database, analysis service resource, production service resource, service resource, storage service resource, data repository, data or information resourceDatabase of a list of insertion sequences isolated from eubacteria and archaea. It is organized into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequences. Although most of the entries have been identified as individual elements, a growing number are included from their description in sequenced bacterial genomes. The search engine permits the retrieval and display of individual and groups of ISs based on a combination of their general features. Two levels of search are available. The simple search option enables the user to sort elements using a limited number of basic items whereas the extensive search offers an additional set of possibilities such as comparisons of the sequences of terminal inverted repeats and a variety of different layout displays. Built in links are provided to: the EMBL sequence database, the NCBI taxonomy database and to the ESF plasmid database. At present, only individual sequences can be downloaded one by one for comparison. An on-line BLAST facility is available and in future versions direct access to additional analytical tools will be provided on line. Direct submission of ISs is encouraged using the on-line form provided.insertion sequence, insertion, sequence, blast, dna, protein sequenceSCR_003020(ISFinder, RRID:SCR_003020)Paul Sabatier University - Toulouse III; Toulouse; France CNRSLast checked downnif-0000-03050
RINSResource, software resourceAn intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of nonhuman sequences in deep sequencing datasets. This is a package recommended for advanced users only.virus, rna-seq, dna-seq, viral integration, clipped-sequence, paired-end, reconstruction, fusion transcript, sequence, perlSCR_003652(RINS, RRID:SCR_003652)Stanford University School of Medicine; California; USA listed by: OMICtoolsLast checked downOMICS_00223
CMKBResource, data or information resource, databaseIt is a database of keys facts about proteins, families, and complexes involved in cell migration. This ongoing project provides a large amount of automated and curated data, collected from numerous online resources that are updated monthly. These data include names, synonyms, sequence information, summaries, CMC research data, reagents, structures, as well as protein family and complex details. CMKB''s ultimate goal is to create a database that will enable the cell migration community to conveniently access significant information about molecules of interest. This will also serve as a stepping stone to pathway analysis and demonstrate how these molecules coordinate with one another during cell adhesion and movement. Sponsors: This resource is supported by the Cell Migration Consortium.cell, migration, knowledgebase, database, protein, family, data, sequence, synonyms, research, reagent, structure, protein, molecule, interest, pathway, adhesion, movementSCR_007229(CMKB, RRID:SCR_007229)Last checked downnif-0000-30312
dCASResource, software resource, web applicationWeb tool to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results. Automates large scale cDNA sequence analysis.automate, large, scale, cDNA, sequence, analysis, BLAST, database, geneSCR_016612(dCAS, RRID:SCR_016612)listed by: NIAIDLast checked down
Functional BiosciencesResource, service resourceA service that provides low cost DNA sequencing. They utilize microfluidic technology.dna, sequencing, sequence, gene, genome, microfluidic, technologySCR_000943(Functional Biosciences, RRID:SCR_000943)listed by: Science ExchangeLast checked downSciEx_9422http://www.scienceexchange.com/facilities/functional-biosciences-inc
PhyloPythiaResource, analysis service resource, data analysis service, service resource, production service resourceData analysis service for accurate phylogenetic classification of variable-length DNA fragments.classification, phyolgenetic, dna fragment, dna, metagenome, sequenceSCR_000540(PhyloPythia, RRID:SCR_000540)listed by: OMICtoolsPMID:17179938Last checked downOMICS_01459
Perlegen/NIEHS National Toxicology: Mouse Genome Resequencing ProjectResource, data set, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, Documented on August 12, 2014. Data, grouped by chromosome, available as flat files for download, of identified DNA polymorphisms (SNPs) in 15 commonly used strains of inbred laboratory mice. Perlegen's SNP, genotype (empirical and imputed), haplotype, trace, and PCR primer data has been compiled with NCBI Mouse Build information to produce data files for public use. Using high-density oligonuclueotide array technology, the study identified over 8 million SNPs and other genetic differences between these strains and the previously sequenced C57BL/6J reference strains (Phase 1). By leveraging data provided by Mark Daly's research team at the Broad Institute, genotypes were also predicted for 40 other common strains (Phase 2). Under an extension to the contract, Eleazar Eskin's group at UCLA has used this data to evaluate SNP associations with phenotypes from the Mouse Phenome Project (the Mouse Phenome Database), and to construct haplotype maps for a total of 94 inbred strains (the Mouse HapMap Project). SNP and genotype positions have been mapped from their original reference coordinates to NCBI Mouse Build 37 coordinates. Note that C57BL6/J strain was not selected for re-sequencing as this data would have been almost entirely redundant with the NCBI reference sequence. Since we did not actually determine genotypes for C57BL6/J, we did not submit genotypes for this strain to dbSNP. However, implicit genotypes for C57BL6/J can be obtained from the reference sequence at each SNP position (the reference allele is the first allele in the ALLELES column). The data is available for download in two different compressed file formats. The files are saved as both PC .zip files and Unix compressed .gz files. At this website, you can: * Learn more about the goals of the Perlegen mouse resequencing project. * Learn more about the array-based resequencing technology used in the project. * Download the SNPs, genotypes, and other data generated by the project, plus sequences of the long-range PCR primers used for SNP discovery. * Browse the mouse genome for SNPs. * View the haplotype blocks within the mouse genome. Mouse Genome Browser The Mouse Genome Browser can be used to visualize genes and the SNPs discovered in this study of genome-wide DNA variation in 15 commonly used, genetically diverse strains of inbred laboratory mice. The reference genome is the C57BL/6J strain NCBI build 37 mouse sequence. In addition to the experimentally-derived genotypes for the original 15 strains, the imputed genotypes for 40 additional inbred mouse strains can also be accessed. Mouse Haplotype Analysis The sequences of 16 commonly used, genetically diverse strains of inbred laboratory mice were analyzed to determine their haplotype structure. The Ancestry Browser shows which ancestral sequence each inbred strain most resembles, along with statistics on the pairwise similarity between the ancestral strains. The Haplotype Viewer shows the haplotype block boundaries and the pairwise similarity for all 56 strains: the 15 used for SNP discovery, the reference strain (C57BL/6J), and the 40 additional strains for which the genotypes were imputed.genetic variation, chromosome, dna, genome, genotype, haplotype, oligonuclueotide, inbred mouse strain, polymorphism, sequence, single-nucleotide polymorphism, c57bl6/jSCR_000726(Perlegen/NIEHS National Toxicology: Mouse Genome Resequencing Project, RRID:SCR_000726)HHSN29120045530C (N01-ES-45530), NIEHSrelated to: Mouse HapMap Imputation Genotype ResourceLast checked downnif-0000-21746
GenoViewerResource, software resourceOpen source viewer / browser software for the SAM / BAM format commonly used in the assembly tasks of Next Generation Sequencing data.next-generation sequencing, sequence, mutation, windows, linux, mac os x, genome, browser, sam, bam, fasta, gff, read error, snp, mnp, insertion, deletionSCR_001203(GenoViewer, RRID:SCR_001203)listed by: OMICtoolsLast checked downOMICS_02146https://github.com/astrid/GenoViewer
Genome TraxResource, service resource, commercial organizationService that provides a comprehensive compilation of variant knowledge that allows you to identify pathogenic variants in human whole genome or exome sequences. It makes it easy to upload a complete genome?s worth of variations and identify the biologically relevant subset of known mutations, mutations that are novel and appear in a candidate disease genes, or mutations that are predicted to have a deleterious effect. The database includes a comprehensive collection of disease causing mutations from HGMD Professional, regulatory sites from TRANSFAC , and disease genes, drug targets and pathways from PROTEOME, as well as pharmacogenomic variants. It integrates the best public data-sets on somatic mutations, allele frequencies and clinical variants, in their most up-to-date version, for a total of more than 165 million annotations. It is possible to identify known pathogenic variants, remove harmless common variants, and obtain deleterious predictions for novel variants. With family data, it is possible to identify variants that are de novo, compound heterozygous only in the offspring. All of the results can be downloaded to Excel for further review. For core facilities and bioinformaticians, the complete underlying data is made available for download and easy integration into custom analysis pipelines. Genome Trax data is optimized to work with many other software packages, such as ANNOVARTM, CLC bio, Alamut, SimulConsult, and Cartagenia.next-generation sequencing, genome, exome, sequence, variation, mutation, pathogenic, databaseSCR_001234(Genome Trax, RRID:SCR_001234)BIOBASE Corporation listed by: OMICtoolsLast checked downOMICS_02109
Integrated DNA Technologies OligoAnalyzerResource, data analysis software, data processing software, software application, sequence analysis software, web application, software resourceWeb-based application for analyzing oligonucleotides. Analysis proceeds after the sequence has been entered and the calculations modified based on target type, oligo concentration, sodium ion concentration, magnesium ion concentration, and dNTP concentration.oligos, oligonucleotides, sequence, web, analyzerSCR_001363(Integrated DNA Technologies OligoAnalyzer, RRID:SCR_001363)Last checked downnif-0000-07754
Neurospora crassa DatabaseResource, data or information resource, databaseIt's strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated and reassembled. This method is standard for microbial genome sequencing, and has been successfully applied to Drosophila. Neurospora is an ideal candidate for this approach because of the low repeat content of the genome. Neurospora crassa Database has expanded the scope of its database by including a mitochondrial annotation, incorporating information from the Neurospora compendium, and assigning NCU numbers to tRNA and rRNAs. They have improved the annotation process to predict untranslated regions and to reduce the number of spurious predictions. As a result, version 3 contains 9,826 genes, 794 fewer than version 2. During the initial phase of a WGS project they sequence both ends of the 4 kb inserts from a plasmid library prepared using randomly sheared and sized-selected DNA. The shotgun reads are assembled by recognizing overlapping regions of sequence and making use of the knowledge of the orientation and distance of the paired reads from each plasmid. Obtaining deep sequence coverage though high levels of sequence redundancy assures that the majority of the genome is represented in the initial assembly and that the consensus sequence is of high quality. Their approach toward the initial assembly was conservative, meaning they would rather fail to join sequence contigs that might overlap each other than risk making false joins between two closely related but non-overlapping genomic regions. Hence, the initial assembly contains many sequence contigs and over time these contigs will increase in size and decrease in number as they are joined together. After shotgun sequencing and assembly there was a second phase of sequencing in which additional sequence was obtained from specific regions that were missing from the original assembly or are recognized to be of low quality in the consensus. The Neurospora crassa sequencing project reflects a close collaboration between the Broad Institute and the Neurospora research community. Principal investigators include Bruce Birren and Chad Nusbaum from the Broad Institute, Matt Sachs at the Oregon Graduate Institute of Science and Technology, Chuck Staben at the University of Kentucky and Jak Kinsey at the Fungal Genetics Stock Center at the University of Kansas Medical Center. In addition, we have a larger Advisory Board made up of a number of Neurospora researchers. Sponsors: They have been funded by the National Science Foundation to sequence the N. crassa genome and make the information publicly available.gene, annotation, compendium, contig, distance, drosophila, genome, mitochondrial, neurospora crassa, plasmid, region, rrna, sequence, trna, untranslatedSCR_001372(Neurospora crassa Database, RRID:SCR_001372)Last checked downnif-0000-20965
ArkDB - Genomes For The Rest of UsResource, data or information resource, databaseThe ArkDB database system aims to provide a comprehensive public repository for genome mapping data from farmed and other animal Species. The system also aims to provide a route in to genomic and other sequence from the initial viewpoint of linkage mapping, RH mapping, physical mapping or - possibly more importantly - QTL mapping data. Sponsors: ArkDB is funded by Biotechnology and Biological Sciences Research Council (BBSRC), UK. Cat, Chicken, Cow, Deer, Duck, Horse, Pig, Quail, Salmon, Sea Bass, Sheep, Turkey, QLT map, Linkage map, RH map, Farm animal, Genome map, Sequence, Mappingduck, farm animal, cat, chicken, cow, deer, genome map, horse, linkage map, mapping, model organism comparative genomic, pig, qlt map, quail, rh map, salmon, sea bass, sequence, sheep, turkeySCR_001838(ArkDB - Genomes For The Rest of Us, RRID:SCR_001838)Roslin Institute Last checked downnif-0000-02568
Sequence Tag Alignment and Consensus Knowledgebase DatabaseResource, data processing software, database, software application, data visualization software, software resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The STACKdb is knowledgebase generated by processing EST and mRNA sequences obtained from GenBank through a pipeline consisting of masking, clustering, alignment and variation analysis steps. The STACK project aims to generate a comprehensive representation of the sequence of each of the expressed genes in the human genome by extensive processing of gene fragments to make accurate alignments, highlight diversity and provide a carefully joined set of consensus sequences for each gene. The STACK project is comprised of the STACKdb human gene index, a database of virtual human transcripts, as well as stackPACK, the tools used to create the database. STACKdb is organized into 15 tissue-based categories and one disease category. STACK is a tool for detection and visualization of expressed transcript variation in the context of developmental and pathological states. The data system organizes and reconstructs human transcripts from available public data in the context of expression state. The expression state of a transcript can include developmental state, pathological association, site of expression and isoform of expressed transcript. STACK consensus transcripts are reconstructed from clusters that capture and reflect the growing evidence of transcript diversity. The comprehensive capture of transcript variants is achieved by the use of a novel clustering approach that is tolerant of sub-sequence diversity and does not rely on pairwise alignment. This is in contrast with other gene indexing projects. STACK is generated at least four times a year and represents the exhaustive processing of all publicly available human EST data extracted from GenBank. This processed information can be explored through 15 tissue-specific categories, a disease-related category and a whole-body indexexonic, expressed, expressed sequence tag (est), expression, fragment, gene, alignment, alternative gene, cdna, clone, cluster, developmental, disease, diversity, genome, homo sapiens, human, isoform, knowledgebase, meta-cluster, mrna, pathological, sequence, tissue, transcript, variant, visualizationSCR_002156(Sequence Tag Alignment and Consensus Knowledgebase Database, RRID:SCR_002156)Last checked downnif-0000-20946
UD Chick EST ProjectResource, biomaterial supply resource, data or information resource, cell repository, material resource, databaseA chicken EST Web site has been created to provide access to the data, and a set of unique sequences has been deposited with GenBank. This site contains over 40,000 EST sequences from the chicken cDNA libraries in the University of Delaware collection. Users can perform keyword searches, BLAST nucleotide sequences against our database, view clusters of similar or overlapping clones, and order clones. The cDNA and gene sequences of many mammalian cytokines and their receptors are known. However, corresponding information on avian cytokines is limited due to the lack of cross-species activity at the functional level or strong homology at the molecular level. To improve the efficiency of identifying cytokines and novel chicken genes, a directionally cloned cDNA library from T-cell-enriched activated chicken splenocytes was constructed, and the partial sequence of 5251 clones was obtained. Sequence clustering indicates that 2357 (42%) of the clones are present as a single copy, and 2961 are distinct clones, demonstrating the high level of complexity of this library. Comparisons of the sequence data with known DNA sequences in GenBank indicate that approximately 25% of the clones match known chicken genes, 39% have similarity to known genes in other species, and 11% had no match to any sequence in the database. Several previously uncharacterized chicken cytokines and their receptors were present in our library. This collection provides a useful database for cataloging genes expressed in T cells and a valuable resource for future investigations of gene expression in avian immunology. Therefore, the Chick EST database was created.gene, avian, cdna, chicken, clone, cytokine, dna, homology, immunology, mammalian, molecular, nucleotide, poultry, receptor, sequence, splenocyte, t cellSCR_002236(UD Chick EST Project, RRID:SCR_002236)University of Delaware; Delaware; USA listed by: One Mind Biospecimen Bank ListingLast checked downnif-0000-20971
AceViewResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER SUPPORTED, 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.est, exon, expression, function, gene, alignment, arabidopsis, cdna, co-alignment, coding, disease, genome, genomic, human, intron, localization, mammal, mouse, mrna, nematode, pathway, phenotype, plant, polyadenylation, promoter, rat, sequence, signal, tissue, transcript, transcriptome, worm, blast, gold standardSCR_002277(AceView, RRID:SCR_002277)NCBI Last checked downnif-0000-21007http://www.ncbi.nih.gov/IEB/Research/Acembly/
Evolutionary Lineage Inferred from Structural AnalysisResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. ELISA is an online database that combines functional annotation with structure and sequence homology modeling to place proteins into sequence-structure-function neighborhoods. The atomic unit of the database is a set of sequences and structural templates that those sequences encode. A graph that is built from the structural comparison of these templates is called PDUG (protein domain universe graph). It introduces a method of functional inference through a probabilistic calculation done on an arbitrary set of PDUG nodes. Further, all PDUG structures are mapped onto all fully sequenced proteomes allowing an easy interface for evolutionary analysis and research into comparative proteomics. ELISA is the first database with applicability to evolutionary structural genomics explicitly in mind.evolutionary, function, functional, analysis, annotation, atomic unit, calculation, comparative, domain, genomic, homology, modeling, place, probabilistic, protein, protein domain and protein classification databases, proteome, proteomic, sequence, structural, structure, templateSCR_002343(Evolutionary Lineage Inferred from Structural Analysis, RRID:SCR_002343)Boston University; Massachusetts; USA Last checked downnif-0000-21141
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