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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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• SciCrunch
• 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 This database is no longer maintained or updated.

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• SciCrunch
• 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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• SciCrunch
• 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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• SciCrunch
• 17 years ago - by Anonymous

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 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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• SciCrunch
• 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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• SciCrunch
• 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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• SciCrunch
• 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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• SciCrunch
• 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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• SciCrunch
• 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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• SciCrunch
• 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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• SciCrunch
• 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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• SciCrunch
• 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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• SciCrunch
• 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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• SciCrunch
• 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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• SciCrunch
• 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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• SciCrunch
• 17 years ago - by Anonymous

DoOP is a database of eukaryotic promoter sequences (upstream regions), aiming to facilitate the recognition of regulatory sites conserved between species. Based on the Arabidopsis thaliana and Homo sapiens genome annotation, we collected the orthologous promoter sequences from Viridiplantae and Chordata species. You can search the database with sequences or text (annotation) to find promoter clusters of different genes. In addition to the sequence and annotation data, the positions of the conserved regions and transcription start sites can be viewed graphically.

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• SciCrunch
• 17 years ago - by Anonymous

Software package for TDT with extended haplotypes in the R language. R is the public domain dialect of S. It should be possible to port this library to the commercial Splus product. The main problem would be translation of the help files. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

A database of human, chimpanzee, mouse, and rat proteases and protease inhibitors, as well as as the growing number of hereditary diseases caused by mutations in protease genes. Analysis of the human and mouse genomes has allowed us to annotate 581 human, 580 chimpanzee, 667 mouse, and 655 rat protease genes. Proteases are classified in five different classes according to their mechanism of catalysis. Proteases are a diverse and important group of enzymes representing >2% of the human, chimpanzee, mouse and rat genomes. This group of enzymes is implicated in numerous physiological processes. The importance of proteases is illustrated by the existence of 99 different hereditary diseases due to mutations in protease genes. Furthermore, proteases have been implicated in multiple human pathologies, including vascular diseases, rheumatoid arthritis, neurodegenerative processes, and cancer. During the last ten years, our laboratory has identified and characterized more than 60 human protease genes. Due to the importance of proteolytic enzymes in human physiology and pathology, we have recently introduced the concept of Degradome, as the complete repertoire of proteases expressed by a tissue or organism. Thanks to the recent completion of the human, chimpanzee, mouse, and rat genome sequencing projects, we were able to analyze and compare for the first time the complete protease repertoire in those mammalian organisms, as well as the complement of protease inhibitor genes. This webpage also contains the Supplementary Material of Human and mouse proteases: a comparative genomic approach Nat Rev Genet (2003) 4: 544-558, Genome sequence of the brown Norway rat yields insights into mammalian evolution Nature (2004) 428: 493-521, A genomic analysis of rat proteases and protease inhibitors Genome Res. (2004) 14: 609-622, and Comparative genomic analysis of human and chimpanzee proteases Genomics (2005) 86: 638-647.

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• SciCrunch
• 17 years ago - by Anonymous