Curator Dashboard

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2015. The CancerGenes resource simplifies the process of gene selection and prioritization in large collaborative projects. CancerGenes combines gene lists annotated by experts with information from key public databases. Gene lists in the CancerGenes resource are from various sources and have been mapped to UCSC canonical gene IDs. Each gene is annotated with gene name(s), functional description, organism, chromosome number, location, Entrez Gene ID, GO terms, InterPro descriptions, gene structure, protein length, transcript count, and experimentally determined transcript control regions, as well as links to Entrez Gene, COSMIC, and iHOP gene pages and the UCSC and Ensembl genome browsers. The user-friendly interface provides for searching, sorting and intersection of gene lists. Users may view tabulated results through a web browser or may dynamically download them as a spreadsheet table.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application for TDT test on markers with more than two alleles using a logistic regression analysis. (entry from Genetic Analysis Software).

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• SciCrunch
• 14 years ago - by Anonymous

Cancer Chromosomes is an integration of three databases, the NCI/NCBI SKY/M-FISH & CGH Database, the NCI Mitelman Database of Chromosome Aberrations in Cancer, and the NCI Recurrent Aberrations in Cancer, which all focus on various aspects of cancer and cancer genes. The goal of the SKY/M-FISH and CGH database is to provide a public platform for investigators to share and compare their molecular cytogenetic data. The database is open to everyone and all users can view an individual investigator''s public data or compare public cases from different investigators. The information in the Mitelman Database of Chromosome Aberrations in Cancer relates chromosomal aberrations to tumor characteristics, based either on individual cases or associations. All the data have been manually culled from the literature. Complete karyotypes, patient characteristics, and references are found in the Mitelman Database of Chromosome Aberrations in Cancer. Users can search all three databases for cytogenetic, clinical, and/or reference information.

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• SciCrunch
• 17 years ago - by Anonymous

Expression profiling and promoter identification software tool for transcriptional network analysis and transcriptome characterization. DeepCAGE, the combination of next-generation sequencing with next generation expression profiling provides unsurpassed solutions for expression profiling and genome annotation. CAGE will be the experimental approach at need to link gene expression and control regions in the genome. With the availability of next-generation sequencing methods, DNAFORM now offers DeepCAGE services. DeepCAGE libraries are prepared for direct analysis by an Illumina/Solexa Sequencer. One sequencing run using one channel on an Illumina/Solexa Sequencer can yield in over 4,000,000 reads per sample. CAGE is based on our full-length cDNA library technology, where an adaptor is ligated to the 5''''-end of full-length cDNAs, which introduces a recognition site for a Class IIs restriction endonuclease adjacent to the 5''''-end of the cDNA. The Class IIs restriction endonuclease, here MmeI, allows for the cloning of short tags as derived from the 5''''-end of transcripts into concatemers for high-throughput sequencing. CAGE tags are further characterized by mapping to genomic sequences, which enables the identification of transcriptional start sites. As such CAGE can contribute to projects in Gene Discovery, Gene Expression, and Promoter Identification. After the genome sequencing projects have provided us with the genetic blueprints for many organisms, new questions have to be answered on how to correlate the observed genotypes with related phenotypes, and how to understand the regulation of genetic information in time and space. The dynamics of living systems and the functional behavior of cells in multicellular organisms has thus become the subject of the emerging field of system biology. Integration of experimental approaches and computer aided theories on a system level will be the fundamental principle to drive systems biology in order to understand the principles behind complex regulatory networks, which will be an ambitious goal requiring new approaches in life sciences. For ordering and additional information, please contact us under contact_at_dnaform.jp

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• SciCrunch
• 17 years ago - by Anonymous

Conformation Angles DataBase is a comprehensive, authoritative and timely knowledge base developed to facilitate retrieval of information related to the conformational angles (main-chain and side-chain) of the amino acid residues present in the non-redundant (both 25% and 90%) data set. The database includes the options of determining the dependency of the conformation angles of a particular residue upon the flanking residues in main-chain, doublet analysis, triplet analysis and analysis of a particular protein structure. It is worth mentioning that for all the options, a user-friendly and convenient Java Graphical User Interface (GUI) has been provided to display the output on the client machine.

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• SciCrunch
• 17 years ago - by Anonymous

BuchneraBase is a database designed to encapsulate and reference information obtained from the complete genome sequence of the gamma-proteobacterium Buchnera sp. APS. We have derived a high quality gene and functional annotation for Buchnera sp. APS. BuchneraBASE also provides for cross-referencing to the genomes of six further symbiotic bacteria for which full sequences are now available: Buchnera sp. SG from the aphid Schizaphis graminum, Buchnera sp. Bp from the aphid Baizongia pistacea, Wigglesworthia glossinidia brevipalpis from the tetse fly Glossina brevipalpis, Blochmannia floridanus from the carpenter ant Camponotus floridanus, Blochmannia pennsylvanicus from the carpenter ant, Camponotus pennsylvanicus, and Baumannia cicadellinicola from the glassy winged sharpshooter, Homalodisca coagulata. We also include Mycoplasma genitalium, with the smallest genome of an organism that can be grown in pure culture. We have constructed BuchneraBASE to facilitate the post-genomic analysis of these bacteria, especially the genomic correlates of co-operative intracellular lifestyles.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Software application that tests for association between genetic marker and disease by examining the transmission of markers from parents to affected offspring. The main features which differ from other similar programs are: (1) It can deal with transmission of multi-locus haplotypes, even if phase is unknown, and (2) Parental genotypes may be unknown. (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.BSD is a database resource that provides information on strains of bacteria with biodegradative properties. The goal of the database is to consolidate and provide rapid access to comparative data on known biodegradative microorganisms and the hazardous substances they degrade as a readily accessible resource for researchers and field practitioners. The database also aims to: # facilitate comparative analyses and highlight deficiencies in our current knowledge base # provide corresponding microbiological data to complement and integrate with the chemical and metabolic data of the University of Minnesota Biocatalysis/ Biodegradation Database and the phylogenetic data of the Ribosome Database Project (RDP-II) # to organize strain data and analyze biocatalysis and biodegradation within a phylogenetic perspective # provide database users a forum for input and contribution and correction of data # serve as a model for the presentation of strain-level, microbial data on the internet To this end, it includes individual data and strain pages, search capabilities, and user input functionality., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

CIPRO is an integrated protein database of the ascidian Ciona intestinalis. It has been developed to provide widespread information of the proteins expressed in the ascidian Ciona intestinalis, especially for the researcher who wants to get advanced and useful information for starting biological and biomedical research. The protein information in CIPRO directly links to gene expression, a tool for peptide mass fingerprinting (PMF), intracellular localization, 3D image of early development, and transgenic resources.

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• SciCrunch
• 17 years ago - by Anonymous

BPS is a database of RNA base pairs with quantitative information on the spatial arrangements of interacting bases, including higher-order base associations, and the context of these interactions in high-resolution crystal structures. The structures are taken from the Nucleic Acid Database (NDB), and the base pairs are identified and characterized with the 3DNA software package. The interactions are classified in terms of residue identities, base-pair positioning, and hydrogen-bonding patterns and related to the structural context in which they occur. A user can browse the atlas of base-pair patterns and carry out searches for patterns of specific types or from specific structures.

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• SciCrunch
• 17 years ago - by Anonymous

Blocks is a database of highly conserved regions of proteins, or Blocks. THe database is no longer maintained or updated and some of its tools are no longer functional. However, Blocks does provide Block Searcher, Get Blocks and Block Maker, aids to detection and verification of protein sequence homology. They compare a protein or DNA sequence to a database of protein blocks (current version), retrieve blocks, and create new blocks, respectively. Users can further view blocks by (keyword or number), search a sequence against the database of blocks, search blocks against each other, or make blocks of their own.

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• SciCrunch
• 17 years ago - by Anonymous

BioThesaurus is a web-based system designed to map a comprehensive collection of protein and gene names to UniProt Knowledgebase protein entries. It covers all UniProtKB protein entries, and consists of several millions of names extracted from multiple resources based on database cross-references in iProClass. The web site allows the retrieval of synonymous names of given protein entries and the identification of ambiguous names shared by multiple proteins. Searches can be done on protein/gene name, organism, or unique identifier.

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• SciCrunch
• 17 years ago - by Anonymous

Bionemo stores manually curated information about proteins and genes directly implicated in biodegradation metabolism. The database includes information on sequence, domains and structures for proteins; and sequence, regulatory elements and transcription units for genes. Bionemo complements other biodegradation databases such as the University of Minessota Biocatalysis/Biodegradation Database, or Metarouter, which focus on the biochemical aspects of biodegradation. Bionemo has been built by manually associating sequences databases entries to biodegradation reactions, using the information extracted from published articles. Information on transcription units and their regulation was also extracted from the literature for biodegradation genes, and linked to the underlying biochemical network.

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• SciCrunch
• 17 years ago - by Anonymous

Biodefense Proteomics Resource Center presents information on Class A-C biodefense organisms. :This list includes Bacillus anthracis, Brucella abortus, Francisella tularensis, salmonella typhi, salmonella typhimurium, Virbio cholerae, Yersinia pestis, Cryptosporidium parvum, Toxoplasma gondii, Avian influenza, SARS, Monkeypox, Vaccinia, and Variola. For each organism, the page provides a general overview of the organism and the diseases it causes, protein (and protein interaction) data, reagents, and data from experiments performed with this organism. Users may also find links to the NCBI Taxonomy center.

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• SciCrunch
• 17 years ago - by Anonymous

The MIPS Ustilago maydis Genome Database aims to present information on the molecular structure and functional network of the entirely sequenced, filamentous fungus Ustilago maydis. The underlying sequence is the initial release of the high quality draft sequence of the Broad Institute. The goal of the MIPS database is to provide a comprehensive genome database in the Genome Research Environment in parallel with other fungal genomes to enable in depth fungal comparative analysis. The specific aims are to: 1. Generate and assemble Whole Genome Shotgun sequence reads yielding 10X coverage of the U. maydis genome 2. Integrate the genomic sequence assembly with physical maps generated by Bayer CropScience 3. Perform automated annotation of the sequence assembly 4. Align the strain 521 assembly with the FB1 assembly provided by Exelixis 5. Release the sequence assembly and results of our annotation and analysis to public Ustilago maydis is a basidiomycete fungal pathogen of maize and teosinte. The genome size is approximately 20 Mb. The fungus induces tumors on host plants and forms masses of diploid teliospores. These spores germinate and form haploid meiotic products that can be propagated in culture as yeast-like cells. Haploid strains of opposite mating type fuse and form a filamentous, dikaryotic cell type that invades plant tissue to reinitiate infection. Ustilago maydis is an important model system for studying pathogen-host interactions and has been studied for more than 100 years by plant pathologists. Molecular genetic research with U. maydis focuses on recombination, the role of mating in pathogenesis, and signaling pathways that influence virulence. Recently, the fungus has emerged as an excellent experimental model for the molecular genetic analysis of phytopathogenesis, particularly in the characterization of infection-specific morphogenesis in response to signals from host plants. Ustilago maydis also serves as an important model for other basidiomycete plant pathogens that are more difficult to work with in the laboratory, such as the rust and bunt fungi. Genomic sequence of U. maydis will also be valuable for comparative analysis of other fungal genomes, especially with respect to understanding the host range of fungal phytopathogens. The analysis of U. maydis would provide a framework for studying the hundreds of other Ustilago species that attack important crops, such as barley, wheat, sorghum, and sugarcane. Comparisons would also be possible with other basidiomycete fungi, such as the important human pathogen C. neoformans. Commercially, U. maydis is an excellent model for the discovery of antifungal drugs. In addition, maize tumors caused by U. maydis are prized in Hispanic cuisine and there is interest in improving commercial production. The complete putative gene set of the Broad Institute''s second release is loaded into the database and in addition all deviating putative genes from a putative gene set produced by MIPS with different gene prediction parameters are also loaded. The complete dataset will then be analysed, gene predictions will be manually corrected due to combined information derived from different gene prediction algorithms and, more important, protein and EST comparisons. Gene prediction will be restricted to ORFs larger than 50 codons; smaller ORFs will be included only if similarities to other proteins or EST matches confirm their existence or if a coding region was postulated by all prediction programs used. The resulting proteins will be annotated. They will be classified according to the MIPS classification catalogue receiving appropriate descriptions. All proteins with a known, characterized homolog will be automatically assigned to functional categories using the MIPS functional catalog. All extracted proteins are in addition automatically analysed and annotated by the PEDANT suite.

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• 17 years ago - by Anonymous

Software package to perform phylogeny based association and localization analysis.Used for association detection and localization of susceptibility sites using haplotype phylogenetic trees. Performs these two phylogeny-based analysis: tests association between candidate gene and disease; pinpoints markers (SNPs) that are putative disease susceptibility loci.

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• SciCrunch
• 14 years ago - by Anonymous

It was created in order to create standard datasets on which the performance of machine learning methods can be compared. The collection contains datasets of sequences and structures, each subdivided into positive/negative training/test sets. Such a subdivision is called a classification task. Typical tasks include the classification of structural domains in the SCOP and CATH databases based on their sequences, as fell as various functional and taxonomic classification tasks. Running a performance evaluation test on an entire database can include many different classification tasks. These ensembles of classification tasks are encoded in a simple matrix format - called the cast matrix or membership table - that specifies the role of each sequence (or structure) in the different calculations. Each column of this matrix is a subdivision of the objects (rows) into positive/negative training/test sets. Typically, a database record contains such an ensemble of classification tasks, encoded in a single cast matrix. In addition, there is a collection of distance matrices that contain an all vs. all comparison of the datasets using methods as BLAST, Smith-Waterman, 3D-comparisons etc. Evaluation of a method on a given database consists of calculating a performance measure such as a receiver operating curve (ROC) AUC value. Results of evaluation are deposited along with the data, each dataset is evaluated at least by one classification method, such as 1NN (nearest neighbour) or SVM (support vector machines), ANN (artificial neural networks), RF (random forests) etc.. There are small datasets meant for program developers, as well as downloadable programs for various classification algorithms.

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• SciCrunch
• 17 years ago - by Anonymous

The Bacterial Carbohydrate Structure DataBase is aimed at provision of structural, bibliographic, taxonomic and related information on bacterial carbohydrate structures. It currently requires Internet Explorer in order to function properly. Two key points of this service are: :* covering - is above 95% in the scope of bacterial carbohydrates. This means the negative search answer remains the valuable information too. :* consistence - we manually check the data, and aim at hight quality error-free content The source of data are Carbbank database (University of Georgia, Athens; structures published before 1995, approx. 4000 records) and manual data posting (structures published after 1995, approx. 3000 records). The scope is bacterial carbohydrates and covers nearly all structures of this class published before 2006. Bacterial means that a structure has been found in bacteria or obtained by modification of those found in bacteria. Carbohydrate means a structure composed of any residues linked by glycosidic, ester, amidic, ketal, phospho- or sulpho-diester bonds, in which at least one residue is a sugar or its derivative. Besides the structure itself, each record includes bibliography, abstract, keywords, biological source, methods used to elucidate the structure, bioactivity, NMR assignment tables and a lot of other information. More details, including a format of records, are available at data submission page. You can search the database by IDs, bibliographic data and keywords, biological source, the fragment of structure and NMR data. The substructure search implies either a query language (expert form) or a structure wizard. The database is cross-linked with GlycoSCIENCES DB, which includes all the data from Carbbank (not only bacterial). This means you can search the substructure you entered in GlycoSCIENCES DB, and each record, which contains a structure also present in Carbbank, has a cross-link to data from GlycoSCIENCES DB, including NMR spectra.

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• SciCrunch
• 17 years ago - by Anonymous

Bcipep is collection of the peptides having the role in humoral immunity. The peptides in the database have varying measure of immunogenicity. This database can assist in the development of methods for predicting B cell epitopes, designing synthetic vaccines, and in disease diagnosis. These peptides lead to the generation of antibodies which combine with antigens and are responsible for the host defense, and can be very useful for subunit vaccine designing. The database has 3031 peptide entries. For each peptide, the user can find a plethora of information, including entry number, peptide sequence, pathogen group, protein source, antigen structure, antibody, etc.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 10, 2011. BANMOKI is a collection of models of 3D structures of all Bacterial Nucleoside Monophosphate Kinases (NMPK), their pre-computed properties and other relevant information. The web server provides information in regard to sequence identity, 3D structure, Enzyme Commission (EC) number, pKa, desolvation penalty, interaction energy with permanent dipoles and the net charge of folded and unfolded states as a function of pH. The database and datasets are searchable by: seq ID name of protein Enzyme commission number pKa desolvation penalty(in pk units) interaction energy with permanent dipoles(in pk units) No. of basic residues No. of acidic residues No. of titratable residues Total no. of residues The web server development and the corresponding scientific work was supported by NATO collaborative grant CBP.EAP.CLG 981749

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• SciCrunch
• 17 years ago - by Anonymous