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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
• 16 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
• 16 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
• 16 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
• 16 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
• 16 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
• 16 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
• 16 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
• 16 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
• 16 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
• 16 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
• 16 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
• 16 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
• 16 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
• 16 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
• 16 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

BACPAC Resources (a BAC Clones Distribution Center) is the distribution arm of their academic laboratory. They operate on a cost-recovery mechanism in order to make the resources generated in their laboratory available to the academic scientific community. While clones and screening services are widely available, library arrays are primarily available to researchers with a scientific need to analyze most clones in the library. This site contains information on currently available BAC and PAC genomic DNA libraries, BAC Clones, PAC Clones, Fosmid Clones, cDNA collections, high-density colony hybridization filters, and BAC and PAC cloning vectors. Protocols used in our laboratory for the hybridization-based screening of colony filters, purification of BAC and PAC DNA, and end-sequencing methodologies, are also provided. BPRC does not list clones, for two reasons: 1)most clones have not been characterized and lack specific data. 2)all clones are part of libraries and all clones from a particular library share common characteristics. Hence, to find out if BPRC has a particular clone, one needs either use Automatic Clone Validation or else find out if the clone is compatible with the range of clone names for a corresponding clone library. Typically (although not always), clone names are derived from the library name. BPRC uses the NCBI-recommended clone nomenclature & library nomenclature. Most arrayed libraries are available in frozen microtiter dish format to academic and non-academic users provided that there is a scientific need for complete-library access. (for instance to annotate, modify or analyze all BAC clones as part of a genome project). Keywords: BAC, Distribution, SUplier, Laboratory, Scientifc, Clone, Screen, Library, Array, Researcher, Research, PAC, Genomic, DNA, Fosmid, cDNA, Hybridization, Filter, Vector, Cloning, Purification, Microtiter,

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 29,2025. Database of functional residues in alpha-helical and beta-barrel membrane proteins. Each protein is identified with its name and source alongwith the Uniprot code. The protein data bank (PDB) codes are also given for available proteins. Different methods and experimental parameters, for example, affinity, dissociation constant, IC50, activity etc. (Details are available at the "Help" page) are given in the database. Further, we have provided the numerical experimental value for each residue (or mutant) in a protein. The experimental data are collected from the literature both by searching the journals as well as with the keyword search at PUBMED. In addition, complete reference is given with journal citation and PMID number. TNFunction is cross-linked with the sequence database, Uniprot, structural database, PDB, and literature database, PubMed. The WWW interface enables users to search data based on various terms with different display options for outputs.

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• SciCrunch
• 16 years ago - by Anonymous

Ontology and database that links plant anatomy, morphology and growth and development to plant genomics data.Plant Ontology Consortium develops, curates and shares controlled vocabularies (ontologies) that describe plant structures and growth and developmental stages, providing semantic framework for meaningful cross species queries across databases. PO is under active development to expand to encompass terms and annotations from all plants.

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• SciCrunch
• 15 years ago - by Anonymous