Curator Dashboard

THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 15, 2017. Software application (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented August 23, 2016. The euHCVdb is oriented towards protein sequence, structure, function analysis and structural biology of the Hepatitis C Virus. It is monthly updated from the EMBL Nucleotide sequence database and maintained in a relational database management system (PostgreSQL). Programs for parsing the EMBL database flat files, annotating HCV entries, filling up and querying the database used SQL and Java programming languages. Great efforts have been made to develop a fully automatic annotation procedure thanks to a reference set of HCV complete annotated well-characterized genomes of various genotypes. This automatic procedure ensures standardization of nomenclature for all entries and provides genomic regions/proteins present in the entry, bibliographic reference, genotype, interesting sites (e.g. HVR1) or domains (e.g. NS3 helicase), source of the sequence (e.g. isolate) and structural data that are available as protein 3D models. The euHCVdb is funded as part of the HepCVax cluster (EC grant QLK2-CT-2002-01329) and viRgil network of excellence (EC grant LSHM-CT-2004-503359).

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• 17 years ago - by Anonymous

ERIC is a resource of annotated enterobacterial genomes. Information is available and accessed through a open web portal uniting biological data and analysis tools. ERIC contains information on Escherichia, Shigella, Salmonella, Yersinia, and other microorgansims. ERIC has recently been moved over to PATRIC: The PATRIC BRC is now responsible for all bacterial species in the NIAID Category A-C Priority Pathogen lists for biodefense research, and pathogens causing emerging/reemerging infectious diseases. For ERIC users, we understand that the resource was valuable to your work. As such, we will be doing our very best to create a useful PATRIC resource to continue supporting your work. We realize that the transition will cause disruptions. However, it is a priority for us to work with established BRC users and communities to identify and prioritize our transition efforts. We have concentrated on the transfer of genomic data for this initial release. We anticipate adding new data, tools, and website features over the next several months. We look forward to working with you during the next 5 years., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• 17 years ago - by Anonymous

The aim of the Ethanol-Related Gene Resource (ERGR) database is to provide a comprehensive and useful gene resource to the Ethanol/Alcohol research community. Currently, the ERGR database contains more than 30 large datasets from literature and 21 mouse QTLs from public database. These data are from 5 organisms (human, mouse, rat, fly and worm) and produced by multiple approaches (expression, association, linkage, QTL, literature search etc). Users can browse or search the database in different levels. Moreover, ERGR provides data integration (union and intersection) and candidate gene selection based on multiple datasets or organisms.

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• 17 years ago - by Anonymous

Database of genes that relate to vertebrate red blood cells. It includes DNA sequence, structural features, protein information, gene expression information and transcription factor binding sites. This database is no longer maintained or updated.

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• 17 years ago - by Anonymous

Epitome is a database of structurally inferred antigenic epitopes in proteins. It includes all known antigenic residues and the antibodies that interact with them, including a detailed description of residues involved in the interaction and their sequence/structure environments. Additionally, Interactions can be visualized using an interface into Jmol. The website also contains specialized software, NLProt, to enable users to extract protein names and sequences from natural language text, and links to several other databases involved in antibody/antigen interactions. antibody/antigen interactions, antigen epitope

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• 17 years ago - by Anonymous

A database that provides information about endocrine networks. Using information about hormones' donor and acceptor cells a network is built that represents hormonal signaling pathways as a bipartite graph comprising hormones and tissues as node classes. The involved components, the intercellular information flow and the inhibition or activation effects are displayed. For each entity a detailed page is available. To represent some known pathways predefined sets are prepared. These sets can be used for quick overview or as starting point for a more complex query It is possible to search for hormones, receptors or tissues and combine several items from different searches in one complex set, from which the network is built.

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• 17 years ago - by Anonymous

Software application (entry from Genetic Analysis Software)

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• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database devoted to the completely sequenced bacterial genomes and the yeast genome. Starting from the sequences available in the "genome" division of GenBank, we have improved and corrected their annotations and structured the flat files using the ACNUC database management system.

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• 17 years ago - by Anonymous

EICO DB is an integrated database for discovery of novel imprinted genes. EICO DB provides candidate imprinted genes by cDNA microarray and single Nucleotide Polymorphisms between MSM and C57BL/6J within RIKEN mouse full-lenght cDNA for validation of imprinting. The tools provided by the website are candidate Imprinted Transcripts by Expression (CITE), MoUse SNP CATalog (MuSCAT), EICO DAS Server, and EICO Wiki.

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• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. ECHO is a web resource of Hepatocellular Carcinoma genes. The fundamental part of EHCO2 is the collections of thirteen gene sets related to HCC. It also contains tools to search by homology, pathway, or phenotype.

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• 17 years ago - by Anonymous

The EcID database (E. coli Interaction Database) provides a common framework for exploring the sizeable amount of protein interaction-related data available for Escherichia coli. EcID integrates information related with functional interactions extracted from the following sources: EcoCyc (metabolic pathways, protein complexes and regulatory information) KEGG (metabolic pathways) and MINT (protein interactions). :It also contains information on protein complexes from the two published high throughput pull down experiments carried out in E. coli, and potential interactions directly extracted from the literature using the web-services associated to the iHOP text-mining system. Additionally, EcID incorporates results from two protein interaction prediction methods based on genomic information (Phylogenetic Profiles and Gene Neighborhoods) and three methods based on analysis of the potential co-evolution of the corresponding protein families (Mirror Tree, In Silico 2 Hybrid and Context Mirror). EcID associates to each predicted pair a confidence score that reflects the reliability of the functional interaction between those two proteins. :In order to provide a global score to combine the predictive power of the prediction methods described above we have integrated in EcID a Bayesian-based classifier. This method includes the scores of five different prediction methods (Phylogenetic Profiles, Gene Neighborhood, Gene Fusion, Mirror Tree and In Silico 2 Hybrid), together with information on a number of simple sequence features. The classifier was trained to predict the type of protein functional associations contained in EcID (derived from regulation data, biochemical pathways, protein complexes and protein physical interactions).

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• 17 years ago - by Anonymous

Database 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.

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• 17 years ago - by Anonymous

It presents an advanced online database for dynamic access to proteomes and two-dimensional (2D) gels. The database was designed to administer complete in silico proteomes and links them with experimental proteomic data in the manner of 2D electrophoresis gels (IPG-Dalt). The 2D gels serve as reference maps in 2D gel analysis as well as tools for navigation of the database to switch between experimental and predicted data. Therefore, all identified spots in the gels are clickable and linked with summarized protein information. The protein information tables contain calculated characteristics, which are often used in proteomics, such as the molecular weight, isoelectric point, codon adaptation index, grand average of hydropathicity, etc. The design of the database permits online extension of gel data and protein attributes without knowledge of any software language. Besides navigation via 2D gels, the clear graphical user interface permits quick and intuitive searching throughout complete proteomes and supports, e.g. the search for proteins with isoelectric points within pH ranges of interest or protein classes (e.g. ribosomal proteins or transporters). The first organism implemented in the database is Lactococcus lactis.

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• 17 years ago - by Anonymous

The iProClass database provides value-added information reports for UniProtKB and unique UniParc proteins, with links to over 90 biological databases, including databases for protein families, functions and pathways, interactions, structures and structural classifications, genes and genomes, ontologies, literature, and taxonomy. iProClass combines both data warehouse and hypertext navigation methods for integrating data, providing a comprehensive picture of protein properties that may lead to novel prediction and functional inference for previously uncharacterized hypothetical proteins and protein groups.

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• 17 years ago - by Anonymous

DSMM provides an easily-searchable source of information about movies showing biomolecular motions that have been generated by computer simulation. All of the movies are available through the internet. Molecules simulated include proteins, DNA, RNA, sugars and lipids. Simulation techniques include Molecular Dynamics, Brownian Dynamics and automated docking procedures.

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• 17 years ago - by Anonymous

DSD is a database of dehydrogenase stereospecificities. It provides stereochemical data and BLASt capability, and also presents other tools to allow users to freely access enzyme stereochemistry data. Users can search using keywords, BLAST, or by enzyme, enzyme type, species, organ/tissue, coenzyme, method, or side.

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• 17 years ago - by Anonymous

Database providing a collection of all the existing polymorphic sequences in the Drosophila genus. It allows users to search for any polymorphic set according to different parameter values of nucleotide diversity. For data collection, diversity measures and updating they use PDA, a pipeline made of a set of Perl modules that automates the process of sequence retrieving, grouping, aligning and estimating diversity parameters from GenBank sequences. Diversity measures, including polymorphism estimates in synonymous and non-synonymous sites, linkage disequilibrium and codon bias, are calculated for each polymorphic set in different functional regions. The database also includes the primary information retrieved from different external sources: the Drosophila publicly available nucleotide sequences (excluding ESTs, STSs, GSSs, working draft and patents) with their annotations and references from GenBank (see the NCBI's Disclaimer and Copyright), additional information of genes and aberrations (from FlyBase), and the cross-references to the PopSet database (from NCBI). The database content is updated daily and records are assigned unique and permanent DPDB identification numbers to facilitate cross-database referencing.

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• 17 years ago - by Anonymous

A database of published cross-link data of the E. coli ribosome. The website provides information on rRNA-rRNA cross-links, rRNA-rProteins cross-links, cross-links between ribosomal proteins, tRNA-ribosome cross-links, growing peptide-ribosome cross-links, factors-ribosome cross-links, and mRNA-ribosome cross-links. All data are presented in tables.

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• 17 years ago - by Anonymous

DPInteract is a database of DNA-binding site matrices. This dataset is being collected with several purposes in mind: 1. Cataloging demonstrated sites and non-sites for E.coli DNA-binding proteins; 2. Aiding the annotation of such sites in other E.coli databases and sequence entries; 3. Interpreting the results of whole-genome in vivo methylation protection experiments; 4. Developing better computational tools for recognizing DNA binding proteins in sequence data.

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• 17 years ago - by Anonymous