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Database dedicated to the analysis of the genome of Escherichia coli. Its purpose is to collate and integrate various aspects of the genomic information from E. coli, the paradigm of Gram-negative bacteria. Colibri provides a complete dataset of DNA and protein sequences derived from the paradigm strain E. coli K-12, linked to the relevant annotations and functional assignments. It allows one to easily browse through these data and retrieve information, using various criteria (gene names, location, keywords, etc.). The data contained in Colibri originates from two major sources of information, the reference genomic DNA sequence from the E. coli Genome Project and the feature annotations from the EcoGene data collection., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• 17 years ago - by Anonymous

coliBASE is a database for comparative genome analysis of Enterobactericaiae, e.g. Escherichia, Shigella etc. coliBASE covers a greater sequence diversity than most other online E. coli resources (which tend to be limited to the K12 genome sequence), and provides novel tools such as the alignment viewer and whole genome viewer that are not available elsewhere. It is supported by a 5 year BBSRC grant until Feburary 2012.

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• 17 years ago - by Anonymous

COGEME is an ongoing BBSRC-funded study to construct a relational database of genomic information from phytopathogenic fungi. This site also hosts microarray data for Blumeria graminis. Expressed sequence tags (ESTs) obtained from eighteen species of plant pathogenic fungi, two species of phytopathogenic oomycete and three species of saprophytic fungi are included here. Hierarchical clustering software was used to classify together ESTs representing the same gene and produce a single contig, or consensus sequence. The unisequence set for each pathogen therefore represents a set of unique gene sequences, each one consisting of either a single EST or a contig sequence made from a group of ESTs. Unisequences were annotated based on top hits against the NCBI non-redundant protein database using blastx.

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• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. DB-PABP is an attempt to document the publicly available experimentally determined polyanion binding proteins (PABPs). The purpose of the database is to provide life scientists who are interested in PA/PABP interactions with a comprehensive data repository, as well as computer scientists with a publicly available dataset to perform knowledge discovery and datamining studies. The database is manually curated. It uses protein annotations from NCBI protein database and literature information is retrieved from PubMed. Whenever applicable, links to NCBI protein database and PubMed are provided so users may access additional information available in these public databases.

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• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 26, 2016. CoC Central is a searchable database of residue conservation data covering the universe of known protein structures. CoC is useful for identifying functionally, kinetically, and thermodynamically important residues. Knowledge of universally conserved positions in protein folds may aid in identifying positions of kinetic or thermodynamic importance in protein folding, as well as those with a functional role.

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• 17 years ago - by Anonymous

CMGSDB is a database whose objective is to investigate gene silencing from a computational perspective using tools of computational biology and bioinformatics. The database is C. elegans centric, although the schema is suitable for any organism and can be extended with minor changes to support multiple organisms. CMGSDB contains details of genome annotation data (chromosomes, genes, coding transcripts), protein structure data (secondary structure, physical properties), microarray expression data (genomewide gene expressions for over 500 microarray experiments), RNA interferance data (RNAi experiment details, phenotypes exhibited by genes in different experiments, phenotype hierarchy and associations between them), protein-protein interaction data, and gene-regulation data.

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• 17 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 June 24, 2013 as per the Miriam database (http://www.ebi.ac.uk/miriam/main/collections/MIR:00000021). The CluSTr database offers an automatic classification of UniProt Knowledgebase and IPI proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons between protein sequences. The database provides links to InterPro, which integrates information on protein families, domains and functional sites from PROSITE, PRINTS, Pfam, ProDom, SMART, TIGRFAMs, Gene3D, SUPERFAMILY, PIR Superfamily and PANTHER. To date (2011), CluSTr contains the following information: * 9,450,285 sequences from UniProt Knowledgebase release 15.6 * 308,281 sequences from IPI * 3,636,831,744 similarities, with pairwise alignments generated on-the-fly * 17,616,060 clusters * Clustering for 972 organisms with completely sequenced genomes. For the full list of the genomes see Integr8 * Putative homologues predictions for the above species. For more information see Homologue Selection at Integr8

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• 17 years ago - by Anonymous

IES-MDS DB is a database of macronuclear and micronuclear genes in spirotrichous ciliates. The database contains information on 440 MDS pairs (each pair composed of the MIC and the MAC version of a given MDS), 392 IES and 361 pointer triples (each pointer has two active copies in the MIC and one copy in the MAC) (7). Out of the 440 MDSs, 235 are scrambled, and 65 are in the opposite strand in the MIC. A total of 320 IESs and 202 pointers are scrambled. For each pair of genes in the database the user can see the micronuclear and macronuclear organization and has the option to see all the MDS, IES and pointer sequences. Another option is to download the MIC sequence with the MDSs and pointers in uppercase and the IESs in lowercase. It is also possible to graphically compare the organization of several genes.

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• 17 years ago - by Anonymous

Ontology for the healthcare common procedure coding system.

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• 13 years ago - by Anonymous

ChromDB is a chromatin database. Three types of sequences are included in the database: genomic-based (predominantly plant sequences); transcript-based (EST contigs or cDNAs for plants lacking a sequenced genome); and NCBI RefSeq sequences for a variety of model animal organisms. The Gene Record Page for any sequence indicates the type of sequence. The broad mission of ChromDB is display, annotate, and curate sequences of two broad functional classes of biologically important proteins: chromatin-associated proteins (CAPs) and RNA interference-associated proteins. Plant proteins are the major focus of the work support by The Plant Genome Research Program (PGRP) of the National Science Foundation. Our intent is to produce intensively curated sequence information and make it available to the research and teaching community in support of comparative analyses toward understanding the chromatin proteome in plants, especially in important crop species. In order to do a comparative analysis, it is necessary to include non-plant proteins in the database. Non-plant genes are not curated to the degree carried out for plants and to automate the process of data import, our non-plant genes are from the RefSeq database of NCBI. We reason that the inclusion of non-plant, model organisms will broaden the relevance and usefulness of ChromDB to the entire chromatin community and will provide a more complete data set for phylogenetic analyses in support of the evolution of the plant chromatin proteome. ChromDB is funded by a grant from the National Science Foundation Plant Genome Research Project(#DBI-0421679).

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• 17 years ago - by Anonymous

Knowledgebase of fusion transcripts collected from various public resources such as the Sanger CGP, OMIM, PubMed, and Mitelman's database. It is an alignment viewer to facilitate examining reliability of fusion transcripts and inferring functional significance., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• 17 years ago - by Anonymous

ChickVD hosts high-quality sequence variation data, variation analysis in the context of chicken genes, cDNAs, chicken orthologs of human disease genes, genetic markers, quantitative trait loci (QTLs) etc . All data are uniquely mapped onto the RJF draft genome and graphically represented in MapView, an efficient visualization tool that allows users to browse sequence variations in the genomic and functional context. The sub-viewer TraceView assists users to view the vivid graphics of the original traces around the detected SNP. Users may query the data by the online search tool and define concrete limitations to extract records that are best suited to their research needs. For the convenience of data presentation in ChickVD, different types of sequence variations (substitutions, insertions or deletions) are all referred as ???SNPs''. ChickVD is updated constantly as more data generated and is under the continued improvement for its content and functionality

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• 17 years ago - by Anonymous

A database of general chemical information. The datasets are comprised of various available chemical datasets annotated with interesting properties to train and test machine-learning prediction and searching methods. Tools provided include ChemicalSearch, Virtual Chemical Space, Reaction Explorer, Datasets, and supplemental material. ChemicalSearch is a tool that allows users to find a chemical by basic criteria like molecular weight and predicted logP, or by the more abstract notion of structural similarity. Virtual Chemical Space is a tool which lets users interactively deconstruct target compounds into component precursors and reconstruct similar building-blocks into combinatorial libraries representing the virtual chemical space near the target compound. Reaction Explorer is a synthesis explorer and mechanism explorer. It provides an interactive system for learning and practicing reactions, syntheses and mechanisms in organic chemistry, with advanced support for the automatic generation of random problems, curved-arrow mechanism diagrams, and inquiry-based learning.

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• 17 years ago - by Anonymous

DOOR (Database of prOkaryotic OpeRons) is an operon database. The operons in the database are based on prediction. The database provides an organism view, gene search, operon search, and operon prediction tools. Currently DOOR has operons for 675 prokaryotic genomes.

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• 17 years ago - by Anonymous

ChemBank is a public, web-based informatics environment that includes freely available data derived from small molecules and small-molecule screens, and resources for studying the data so that biological and medical insights can be gained. ChemBank is intended to guide chemists synthesizing novel compounds or libraries, to assist biologists searching for small molecules that perturb specific biological pathways, and to catalyze the process by which drug hunters discover new and effective medicines. ChemBank stores an increasingly varied set of cell measurements derived from, among other biological objects, cell lines treated with small molecules. Analysis tools are available and are being developed that allow the relationships between cell states, cell measurements and small molecules to be determined. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the ICG in collaborations involving biomedical researchers worldwide. These scientists have agreed to perform their experiments in an open data-sharing environment. The goals of ChemBank are to provide life scientists unfettered access to biomedically relevant data and tools heretofore available almost exclusively in the private sector. We intend for ChemBank to be a planning and discovery tool for chemists, biologists, and drug hunters anywhere, with the only necessities being a computer, access to the Internet, and a desire to extract knowledge from public experiments whose greatest value is likely to reside in their collective sum.

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• 17 years ago - by Anonymous

An evidence taxonomy for pharmacologic studies that, when combined with a set of inclusion criteria, enable drug experts to specify what their confidence in a drug mechanism assertion would be if it were supported by a specific set of evidence.

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• 13 years ago - by Anonymous

CGED (Cancer Gene Expression Database) is a database of gene expression profile and accompanying clinical information. The data of CGED were obtained through collaborative efforts to identify genes of clinical importance. This database offers graphical presentation of expression and clinical data with similarity search and sorting functions. CGED includes data on breast (prognosis and docetaxel data sets), colorectal, hepatocellular, esophageal, thyroid, and gastric cancers (updated in March 2007). Genes in CGED can be searched by: 1) gene names or identifiers, or 2) gene ontology terms or keywords in functional annotations in the SwissProt, or 3) cancer types and its clinical factors, or 4) gene expression differentials based on p value or q value.

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• 17 years ago - by Anonymous

CSRDB is a bioinformatics resource for cereal crops consisting of large-scale datasets of maize and rice and small RNA sequences. The sequences were generated by 454 Life Science sequencing. The small RNA sequences have been mapped to the rice genome and available maize genome sequence and are presented in two genome browser datasets using the Generic Genome Browser. Potential target sequences representing mature mRNA sequences have been predicted using the FASTH software from the Zuker lab. and access to the resulting small RNA target pair (SRTP) dataset has been made available through a mysql based relational database. Within the genome browser the small RNAs have links to the SRTP database that will return a list of potential targets. The SRTP database may also be searched independently using both small RNA and target transcript queries. Data linking and integration is the main focus of this interface and to this aim links are present in the SRTP results pages back to the browser and the SRTP database as well as external sites.

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• 17 years ago - by Anonymous

Centrosome:db contains a set of human genes encoding proteins that are localized in the centrosome, either as centrosome constituents or as centrosome visitors. Genes have been considered as centrosomal on the basis of different kinds of evidences including high-throughput proteomics assays, annotations in public databases and orthology relationships to centrosomal genes in closely related species (e.g. mouse). For each of these human genes we have compiled information from various sources such as Ensembl, OMIM, HPRD, SNPs, GeneOntology or Compara, among others. Orthologs in other species, ranging from yeast to mammals, have been also included in centrosome:db. The domain structure of all the associated peptides has been characterized based on the domain profiles of the Pfam and Superfamily databases (scanned with the RPS-BLAST program) and on the coiled-coil predictions of the COILS program. You can browse the database by: :* Searching with a gene name, database identifier or submmiting full text queries (uniprot, ensembl, hgnc, entrez, ipi and refseq identifiers are supported) :* Searching for a given domain in a particular specie (or all species) :* Accesing the orthology information related to a gene :* Comparing your own sequence with those in centrosome:db :* Retrieve all the human centrosomal genes based on their evidences

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• 17 years ago - by Anonymous

A database to provide cleansed EST sequences of classified dbEST libraries. All dbEST libraries were classified according to organism, sequencing center, and eVOC ontologies (for human libraries). For each dbEST library, we provide three different EST sequences: raw, pre-cleansed, and user-cleansed. pre-cleansed ESTs are obtained from major contamination databases and cleaned of contaminated sequences. User-cleansed ESTs, however, involve the use of an automatic user-cleansing pipeline, in which sequences in a user-selected library are cleansed on-the-fly according to user-input options. CleanEST contains 62,008,259 EST sequences (24,000 libraries) with contamination information.

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• 17 years ago - by Anonymous