Curator Dashboard

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It is dedicated to the nuclear genes specifying the enzymes, structural proteins, and other proteins, many still not identified, involved in mitochondrial biogenesis and function. MitoDat highlights predominantly human nuclear-encoded mitochondrial proteins, although it also includes proteins from other animals in addition to those currently known only from yeast and other fungal mitochondria, as well as from plant mitochondria. he database consolidates information from various biological databases, eg., GenBank, SwissPro, Genome Data Base (GDB), Online Mendelian Inheritance in Man (OMIM), et al. Because the mitochondrion has a central role in cellular metabolism, it is involved in many human diseases. This database should help us in studying these diseases. We are also hyperlinked to the Report of the committee on human mitochondrial DNA, maintained by the Wallace group at Emory. It can be accessed here and also from the results when searching mitoDat for mitochondrially encoded genes. The Report of the committee on human mitochondrial DNA is currently the most comprehensive source of information on mitochondrial DNA mutations, other defects, and disorders in which the mitochondrial DNA deficiencies have been associated.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A web site dedicated to providing links to mitochondrial data and databases, as well as links to other mitochondrial sites and relevant information. It provides links to databases, complete mitochondrial genomes, genome maps, and publications.

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• SciCrunch
• 17 years ago - by Anonymous

It contains predictions of precursor miRNA genes covering several animal genomes combining orthology and a Support Vector Machine. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline. The current release of miROrtho covers 46 animal genomes. We provide homology extended alignments of already known miRBase families and putative miRNA families exclusively predicted by our SVM and orthology pipeline.

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• SciCrunch
• 17 years ago - by Anonymous

An integrated database of positional relationships between animal miRNAs and genomic annotation sets and animal miRNA targets according to combinations of widely used target prediction programs. miRGen has three connected interfaces which query this data. The Genomics interface allows the user to explore where whole-genome collections of miRNAs are located with respect to UCSC genome browser annotation sets such as Known Genes, Refseq Genes, Genscan predicted genes, CpG islands, and pseudogenes. The Targets interface provides access to unions and intersections of four widely used target prediction programs, and experimentally supported targets from TarBase. The Clusters interface provides predicted miRNA clusters at any given inter-miRNA distance, and provides specific functional information on the targets of miRNAs within each cluster.

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• SciCrunch
• 17 years ago - by Anonymous

A resource dedicated to the distribution of information about nucleotide variation found in the PHEX gene, the majority of which are found in patients with X-linked hypophosphatemia. Users can search by mutation, phenotype, or author, or submit their own mutations.

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• SciCrunch
• 17 years ago - by Anonymous

A database of the molecular structure and functional network of the entirely sequenced, filamentous fungus Neurospora crassa. The underlying sequence is the release 7 of the high quality draft sequence of the Broad Institute. The goal 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 database contains the manually modelled gene set generated in the German Neurospora genome project and is combined with Broad calls from release 7 version 3.

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• SciCrunch
• 17 years ago - by Anonymous

Database of compiled, public, deep sequencing miRNA data and several novel tools to facilitate exploration of massive data. The miR-seq browser supports users to examine short read alignment with the secondary structure and read count information available in concurrent windows. Features such as sequence editing, sorting, ordering, import and export of user data are of great utility for studying iso-miRs, miRNA editing and modifications. miRNA����??target relation is essential for understanding miRNA function. Coexpression analysis of miRNA and target mRNAs, based on miRNA-seq and RNA-seq data from the same sample, is visualized in the heat-map and network views where users can investigate the inverse correlation of gene expression and target relations, compiled from various databases of predicted and validated targets.

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• SciCrunch
• 17 years ago - by Anonymous

A manually curated database, aims at providing a comprehensive resource of miRNA deregulation in various human diseases. Each entry in the miR2Disease contains detailed information on a miRNA-disease relationship, including miRNA ID, disease name, a brief description of the miRNA-disease relationship, miRNA expression pattern in the disease state, detection method for miRNA expression, experimentally verified miRNA target gene(s), and literature reference . All entries can be retrieved by miRNA ID, disease name or target gene. miR2Disease will be updated bimonthly. miR2Disease sincerely looks forward to recently established relationship between miRNA and human diseases to be submitted.

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• SciCrunch
• 17 years ago - by Anonymous

It aims to provide a data and information resource for individual plant species. In addition PlantsDB provides a platform for integrative and comparative plant genome research. It provides information on monocots and dicots, a comparative map viewer, and other specialized databases.

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• SciCrunch
• 17 years ago - by Anonymous

Health Research Funding is designed to bring researchers with peer-reviewed, worthwhile, unfunded projects together with patient advocacy organizations and other funding sources. Working together, we hope to foster the funding of new research that will provide hope to millions of people in this country with chronic diseases and disabilities. * We invite researchers with promising projects that have been scored but not funded by the NIH to submit their abstracts. By registering, you will be able to search for information about organizations that fund research and their requests for abstracts. * Researchers with proposals that have been peer-reviewed but not funded by a NHC member patient advocacy organization may also register. The National Health Council (NHC) developed this site with input from the National Institutes of Health (NIH), the nation''s medical research agency.

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• SciCrunch
• 16 years ago - by Anonymous

OPD is a public database for storing and disseminating mass spectrometry based proteomics data. It covers Escherichia coli, Homo sapiens, Saccharomyces cerevisiae, Mycobacterium smegmatis, and Mus musculus. The database currently contains roughly 3,000,000 spectra representing experiments from these 5 different organisms. The mirror url is provided below as the OPD website is no longer functional (http://bioinformatics.icmb.utexas.edu/OPD/).

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• SciCrunch
• 17 years ago - by Anonymous

It analyzes protein queries for the presence of short functional motifs that, in at least one protein, has been demonstrated to be involved in posttranslational modifications (PTM), binding to other proteins, nucleic acids, or small molecules, or proteins trafficking. The low sequence complexity of motifs, suggest that "false positive" motifs may occur and any prediction made by MnM should be experimentally tested. To aid in the selection of motifs, MnM ranks motifs based on frequencies in proteomes, protein surface prediction, and evolutionary conservation. Using annotation of motifs in the Swiss-Prot database, we have found that higher scores are globally correlated with experimentally validated motifs when compared to a similar analysis using randomized motifs with the same amino acid composition. We suggest that the known biology of the protein of interest and of motifs be used in selecting motifs for experimental study.

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• SciCrunch
• 17 years ago - by Anonymous

In an effort to strongly support the collaborative nature of scientific research, BIOBASE offers access to their tools. Programs that are available through this portal are: * AliBaba 2.1: AliBaba2 is a program for predicting binding sites of transcription factor binding sites in an unknown DNA sequence. Therefore it uses the binding sites collected in TRANSFAC. AliBaba2 is currently the most specific tool for predicting sites. * Boxshade 3.3.1: Pretty Printing and Shading of Multiple-Alignment files. * ClustalW 1.8: ClustalW Multiple Sequence Alignment Program. * Dialign2.0: Multiple Sequence Alignment Program. * F-Match 1.0: F-MATCH is a program for identifying statistically overrepresented Transcription Factor Binding Sites (TFBS) in a set of sequences compared against a control set, assuming a binomial distribution of TFBS frequency. The program reads MATCH output files for the query and control sets. F-Match uses a library of mononucleotide weight matrices from TRANSFAC 6.0 * Match 1.0 Public: Match is designed for searching potential binding sites for transcription factors (TF binding sites) nucleotide sequences. MatchTM uses a library of mononucleotide weight matrices from TRANSFAC 6.0 * molwSearch 1.0: Search for transcription factors with a certain molecular weight. * P-Match 1.0: P-Match is a new tool for identifying transcription factor binding sites (TF binding sites) in DNA sequences. It combines pattern matching and weight matrix approaches thus providing higher accuracy of recognition than each of the methods alone. P-Match uses a library of mononucleotide weight matrices from TRANSFAC 6.0 along with the site alignments associated with these matrices. * Patch 1.0: Search for potential transcription factor binding sites in your own sequences with the pattern search program using TRANSFAC 6.0 public sites. * m2transfac 1.0: m2transfac is a PWM-PWM alignment interface for the TRANSFAC(R) database. For given user motifs, m2transfac reports all non-overlapping pairwise alignments to a TRANSFAC(R) matrix which satisfy a specified threshold. * MatrixCatch 2.7: The MatrixCatch tool is designed for searching potential composite elements (CEs) for transcription factors (TFs) in any DNA sequence, which may be of interest. MatrixCatch uses a library of CE matrix models, which were compiled on a basis of experimentally identified CEs collected in TRANSCOMPEL database and mononucleotide weight matrices for single TF-binding sites collected in TRANSFAC 6.0 public database. * Composite Module Analyst (CMA) 1.0: CMA reads output of Match program and applies a genetic algorithm in order to define promoter models based on the composition of transcription factor binding sites and their pairs. * PolyA Scan 0.000707: Scanning a Sequence for potential Polyadenylation Sites. * ReadSeq 2.0: ReadSeq reads and writes nucleic/protein sequences in various formats. * SignalScan: Analysis of DNA Sequences for known Eukaryotic Signals * SbBlast 1.0: Search Tool for Sequence Search in the S/MARt Binder Database. SbBlast makes use of the BLAST Sequence Similarity Search Tool - Version 2.0.13 (May-26-2000). * SnpFind 0.3: SNPFIND is a tool for searches in the Database of Single Nucleotide Polymorphisms. The search algorithm used for the database search is the BLAST algorithm. * TfBlast 0.1: Search Tool for Sequence Search in the TRANSFAC Factor Table. SbBlast makes use of the BLAST Sequence Similarity Search Tool - Version 2.0.13 (May-26-2000).

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• SciCrunch
• 16 years ago - by Anonymous

This repository contains full data from MHCPEP database, and selected data including independent data sets of proteins and protein fragments, non-binding peptides, lists of T-cell epitopes, and recommendations for scaling and comparison of performance of prediction systems. It can be used in conjunction with IEDB data sets for the development of advanced machine learning and pattern recognition solutions.

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• SciCrunch
• 17 years ago - by Anonymous

The MHCBN is a curated database consisting of detailed information about Major Histocompatibility Complex (MHC) Binding,Non-binding peptides and T-cell epitopes. The version 4.0 of database provides information about peptides interacting with TAP and MHC linked autoimmune diseases.

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• SciCrunch
• 17 years ago - by Anonymous

The MHC-Peptide Interaction Database version T (MPID-T) is a new generation database for sequence-structure-function information on T cell receptor/peptide/MHC interactions. It contains all structures of TcR/pMHC and pMHC complexes, with emphasis on the structural characterization of these complexes. MPID-T will facilitate the development of algorithms to predict whether a peptide sequence will bind to a specific MHC allele. The database has been populated with the data from the Protein Data Bank(PDB). The data from the PDB is manually verified and classified, after which each structure is analysed for atomic interactions relevant to MHC-Peptide complex.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2019.Database for annotated mouse proteins and their occurrence in protein networks. It contains cDNA and protein sequences, annotation, gene models and mapping, FunCat, UCSC Genome Viewer, SIMAP, pseudogenes (Genome Viewer Track), InterPro, and splice variants. Protein function annotation is performed using the Functional Catalogue (FunCat) annotation scheme, which is a hierarchically structured classification system. To provide up-to-date similarity search results and InterPro domain analyses, the protein entries are interconnected with the SIMAP database. The gene models are based on the RefSeq mouse cDNAs. The work of our group is focussed on the annotation of biological systems. Therefore, results from the Mammalian Protein-Protein Interaction Database and the Comprehensive Resource of Mammalian Protein Complexes are linked to the MfunGD dataset. Links to external resources are also provided. MfunGD is implemented in GenRE, a J2EE based component oriented multi-tier architecture.

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• SciCrunch
• 17 years ago - by Anonymous

A database of information on nuclear receptors. Included in the database are sequence information, structural information, and mutation data. Users can BLAST sequences, view 2D structural data, see the chromosomal location of nuclear receptors genes, and utilize other tools found on the website.

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• SciCrunch
• 17 years ago - by Anonymous

metaTIGER is a collection of metabolic profiles and phylogenomic information on a taxonomically diverse range of eukaryotes. Phylogenomic information is provided by 2,257 large phylogenetic trees which can be interactively explored. High-throughput tree analysis can also be carried out to identify trees of interest, e.g. trees containing horizontal gene transfers. metaTIGER also provides novel facilities for viewing and comparing the metabolic profiles.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 24, 2013. Database and Browser containing quantitative information on all the metal-containing sites available from structures in the PDB distribution. This database contains geometrical and molecular information that allows the classification and search of particular combinations of site characteristics, and answer questions such as: How many mononuclear zinc-containing sites are five coordinate with X-ray resolution better than 1.8 Angstroms?, and then be able to visualize and manipulate the matching sites. The database also includes enough information to answer questions involving type and number of ligands (e.g. "at least 2 His"), and include distance cutoff criteria (e.g. a metal-ligand distance no more than 3.0 Angstroms and no less than 2.2 Angstroms). This database is being developed as part of a project whose ultimate goal is metalloprotein design, allowing the interactive visualization of geometrical and functional information garnered from the MDB. The database is created by automatic recognition and extraction of metal-binding sites from metal-containing proteins. Quantitative information is extracted and organized into a searchable form, by iterating through all the entries in the latest PDB release (at the moment: September 2001). This is a comprehensive quantitative database, which exists in SQL format and contains information on about 5,500 proteins.

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• SciCrunch
• 17 years ago - by Anonymous