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THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Set of databases and tools that handle genomic and metagenomic sequences in their environmental contexts.Includes geographic information system to systematically store and analyse marine genomic and metagenomic data in conjunction with contextual information; environmental genome browser with fast search functionalities; database with precomputed analyses for selected complete genomes; database and tool to classify metagenomic fragments based on oligonucleotide signatures.

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• SciCrunch
• 17 years ago - by Anonymous

Comprehensive collection of spatially interacting motifs in proteins. Interacting motif database lists interacting motifs that are identified for all structural entries in PDB. Conserved patterns or finger prints are identified for individual structural entries and also grouped together for reporting common motifs shared among all superfamily members.

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• SciCrunch
• 17 years ago - by Anonymous

Model organism database for the social amoeba Dictyostelium discoideum that provides the biomedical research community with integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase houses the complete genome sequence, ESTs, and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome to provide a ''''reference genome'''' in the Amoebozoa clade. They highlight several new features in the present update: (i) new annotations; (ii) improved interface with web 2.0 functionality; (iii) the initial steps towards a genome portal for the Amoebozoa; (iv) ortholog display; and (v) the complete integration of the Dicty Stock Center with dictyBase. The Dicty Stock Center currently holds over 1500 strains targeting over 930 different genes. There are over 100 different distinct amoebozoan species. In addition, the collection contains nearly 600 plasmids and other materials such as antibodies and cDNA libraries. The strain collection includes: * strain catalog * natural isolates * MNNG chemical mutants * tester strains for parasexual genetics * auxotroph strains * null mutants * GFP-labeled strains for cell biology * plasmid catalog The Dicty Stock Center can accept Dictyostelium strains, plasmids, and other materials relevant for research using Dictyostelium such as antibodies and cDNA or genomic libraries.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 11th,2023. The database HOX Pro contains information about organization, functions and evolution of gene ensembles, key roles in which play homeobox-genes. It is aimed at: 1. analysis and classification of regulatory and coding regions in diverse homeobox and related genes; 2. describing mutations and knock-outs of hox-genes, as well as hereditary diseases related to these genes; 3. graphical representation, comparisons and classification of hox-genes expression patterns and profiles (sea urchin blastula, Drosophila blastoderm and imaginal discs, vertebrate limbs, mammalian brain, human EC cells); 4. comparative analysis of organization of hox-based genetic networks the nematode Caenorhabditis elegans the sea urchins Strongylocentrotus purpuratus and other echinids, the fruit flies Drosophila melanogaster and D.virilis, the vertebrates chicken and mouse; 5. analysis of phylogeny and evolution of homeobox genes and clusters.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 10th,2023. Commercial provider of cognitive assessments, including their proprietary database, the Brain Resource International Database (BRID) that allows users to quantify individual differences in brain function, compare individual performance against peers, and provide a robust frame of reference for clinical assessment and treatment decisions. Database provides evidence for brain behavior connection so important to reliably enabling optimal solutions for mental health and wellbeing. It powers all Brain Resource products.

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• SciCrunch
• 17 years ago - by Anonymous

A database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. Users can find links to the PDB coordinates of virus structures, rendered structural images of viral subunits, capsids, and crystal contacts, as well as find basic information such as family, genus, and number of subunits of different viruses. Viperdb includes powerful search utilities, links to other relevant databases, background information on virus capsid structure, and useful database interface tools. It describes various icosahedral virus capsid structures in the Protein Data Bank (PDB) in terms of their complete capsids, detailed structural and computational analysis. Additionally, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The protomeric (asymmetric unit) coordinates were transformed and stored in a single icosahedral convention (2(Z)-3-5-(X)2). Coordinates (sometimes) were further processed by rearranging the nucleic acid residues, hetero atoms, and water molecules (if present) at the end of the protein chains for the ease of further analysis. Structures are classified in terms of their quasi-symmetry (e.g. T=3, T=4, T=7) and pseudo-symmetry (e.g., P=3).Tools are being developed to study the capsids in terms of structural, energetic and assembly aspects . The derived results are made available throught this website. The site is being developed as part of the training, service and dissemination component of the NIH Research Resource: Multiscale Modeling Tools for Structural Biology (MMTSB).

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• SciCrunch
• 17 years ago - by Anonymous

Study to surveyed structures of protein-protein interfaces in PDB to carry out structural comparisons of interfaces. Structural comparisons of protein-protein interfaces.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE documented June 5, 2013 Proteome Analyst (PA) is a publicly available, high-throughput, web-based system for predicting various properties of each protein in an entire proteome. Using machine-learned classifiers, PA can predict, for example, the GeneQuiz general function and Gene Ontology (GO) molecular function of a protein. In addition, PA is currently the most accurate and most comprehensive system for predicting subcellular localization, the location within a cell where a protein performs its main function. Two other capabilities of PA are notable. First, PA can create a custom classifier to predict a new property, without requiring any programming, based on labeled training data (i.e. a set of examples, each with the correct classification label) provided by a user. PA has been used to create custom classifiers for potassium-ion channel proteins and other general function ontologies. Second, PA provides a sophisticated explanation feature that shows why one prediction is chosen over another. The PA system produces a Naïve Bayes classifier, which is amenable to a graphical and interactive approach to explanations for its predictions; transparent predictions increase the user's confidence in, and understanding of, PA.

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• SciCrunch
• 17 years ago - by Anonymous

Database of experimentally verified IRES structures. Presents information about experimentally studied Internal Ribosome Entry Site segments.

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• SciCrunch
• 17 years ago - by Anonymous

Publicly available database of summary level findings from genetic association studies in humans, including genome wide association studies (GWAS). Previously named HGBASE, HGVbase and HGVbaseG2P.

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• SciCrunch
• 17 years ago - by Anonymous

Collection of pre-calculated evolutionary conservation profiles for proteins of known structure in the Protein DataBase (PDB).Enables flexibility in setting the parameters of the calculation, and accepts optional uploads of atomic coordinates, multiple sequence alignments, and phylogenetic trees for use in the calculation of conservation profiles

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• SciCrunch
• 17 years ago - by Anonymous

A web portal devoted to genomic information and tools. It includes lists of techniques, databases of genes and microarrays, annotation tools and resources, functional information, bibliographic information, and supporting resources.

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• SciCrunch
• 17 years ago - by Anonymous

Software tool collection for analysis of FMRI, MRI and DTI brain imaging data. It runs on Apple and PCs (both Linux, and Windows via a Virtual Machine). FSL is completely self-contained. Most of the tools can be run both from the command line and through graphical interfaces. Tools include: STRUCTURAL TOOLS BET - Brain Extraction Tool - segments brain from non-brain in structural and functional data. SUSAN - Nonlinear noise reduction. FAST - FMRIB''s Automated Segmentation Tool - brain segmentation (into different tissue types) and bias field correction. FLIRT - FMRIB''s Linear Image Registration Tool - linear inter- and intra-modal registration. FUGUE - Unwarps distortion in EPI images using B0 field maps. SIENA - Structural brain change analysis, for estimating brain atrophy. (BET, FLIRT and FUGUE are also used in FMRI analysis) FUNCTIONAL TOOLS FEAT - Advanced FMRI analysis with easy-to-use yet powerful GUI. Includes all necessary preprocesing, model-based and semi-model-free statistical analysis, automatic registration to structural and/or standard space, and fixed- and random-effects group statistics. MCFLIRT - FMRI motion correction. MELODIC - ICA-based model-free analysis of FMRI (and other 4D) data. :An excellent set of tools for many types of analysis of neuroimaging structural and functional data

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 09, 2013. DCViewer opens img/hdr file pairs, allows browsing along X,Y Z and Time dimensions (if present) with configurable color and intensity settings. The files can be opened remotely from URLs if desired. Entire directories of files can be automatically combined into a single image. Multiple images can be layered for comparison.

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• SciCrunch
• 17 years ago - by Anonymous

Organization portal for neuromuscular disease community and contains comprehensive listing of biological and clinical aspects of neuromuscular disorders.This knowledge base contains information on the physiology, structure of ion channels, neurotransmitters, neuroreceptors, and associated diseases. Major categories include DISORDERS & SYNDROMES, INDEXES, NEUROMUSCULAR EVALUATION, ANTIBODY TESTING and NEUROMUSCULAR DIVISION.

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• SciCrunch
• 17 years ago - by Anonymous

Functional genomics data repository supporting MIAME-compliant data submissions. Tools are provided to help users query and download experiments and curated gene expression profiles. These data include microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted.

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• SciCrunch
• 17 years ago - by Anonymous

Anatomical atlas about structural anatomy of Caenorhabditis elegans. Provides simple interface allowing user to easily navigate through every anatomical structure of worm. Contains set of images which can be sorted by different characteristics: sex, genotype, age, body portion or tissue type. Includes links to other major worm websites and databases. Application for viewing and downloading thousands of unpublished electron micrographs and associated data. These images have been generated by several labs in the C. elegans community, including the MRC, the Hall lab (Center for C. elegans Anatomy), and the Culotti and Riddle labs.

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• SciCrunch
• 17 years ago - by Anonymous

Detailed multidimensional digital multimodal atlas of C57BL/6J mouse nervous system with data and informatics pipeline that can automatically register, annotate, and visualize large scale neuroanatomical and connectivity data produced in histology, neuronal tract tracing, MR imaging, and genetic labeling. MAP2.0 interoperates with commonly used publicly available databases to bring together brain architecture, gene expression, and imaging information into single, simple interface.Resource to visualise mouse development, identify anatomical structures, determine developmental stage, and investigate gene expression in mouse embryo. eMouseAtlas portal page allows access to EMA Anatomy Atlas of Mouse Development and EMAGE database of gene expression.EMAGE is freely available, curated database of gene expression patterns generated by in situ techniques in developing mouse embryo. EMA, e-Mouse Atlas, is 3-D anatomical atlas of mouse embryo development including histology and includes EMAP ontology of anatomical structure, provides information about shape, gross anatomy and detailed histological structure of mouse, and framework into which information about gene function can be mapped.

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• SciCrunch
• 17 years ago - by Anonymous

Software application (entry from Genetic Analysis Software)

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• SciCrunch
• 13 years ago - by Anonymous

Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software)

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• SciCrunch
• 13 years ago - by Anonymous