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Het-PDB Navi. v1.5.5: Het-PDB Navi. is a navigator of small molecules in Protein Data Bank which is called heterogen atoms or in short hetatoms

Het-PDB Navi. v1.5.5: Het-PDB Navi. is a navigator of small molecules in Protein Data Bank which is called heterogen atoms or in short hetatoms | bioinformatics-databases | Scoop.it

Het-PDB Navi. is a navigator of small molecules in Protein Data Bank which is called heterogen atoms or in short hetatoms.


PDB is a database for protein three-dimensional structures, but the data in PDB are often obtained with bound non-standard components such as DNA, RNA, ATP, GTP, PLP and so forth. As number of proteins in PDB increases, we realized that a wealth of information for small molecule-protein interactions is buried in PDB.


The interactions found in PDB can be treated as a general template for interaction between a protein and a small molecule, such as ATP, GTP and drugs.


We have, hereby, launched Het-PDB Navi. as a starter for classification and data retrieval system of protein-small molecule interactions from PDB.


The database is focused on small molecules and does not treat macromolecules such as DNA and RNA. The database was initially developed at Nagoya University in 1999, and transferred to Nagahama Institute of Bio-Science and Technology in 2003.


The database has been maintained by Prof. Mitiko Go's laboratory from the beginning.

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HEXEvent - A database of Human EXon splicing Events

HEXEvent - A database of Human EXon splicing Events | bioinformatics-databases | Scoop.it

HEXEvent is a free database that provides a list of human internal exons and reports all their known splice events based on EST information from the UCSC Genome Browser . This list can be restricted by the user to either only a specific region in the genome (by specifying the chromosome, the strand and the start and end position), to a whole chromosome or to a group of genes. Furthermore, exons can be filtered according to their splicing type (constitutive exons, cassette exons and exons with one or more alternative 3' and/or 5' splice sites).


In order to extract a customized set of exons, the user-specific definitions of exon types can be fixed. The user needs to specify in what fraction of ESTs an exon is allowed to be alternatively spliced in order to still be called constitutive. Furthermore, the user can restrict the set of requested cassette exons by a certain upper inclusion level, which, for instance, is useful when only looking for low-inclusion exons.

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Hembase: browser and genome portal for hematology and erythroid biology

Hembase: browser and genome portal for hematology and erythroid biology | bioinformatics-databases | Scoop.it

Hembase (http://hembase.niddk.nih.gov) is an integrated browser and genome portal designed for web-based examination of the human erythroid transcriptome. To date, Hembase contains 15752 entries from erythroblast Expressed Sequenced Tags (ESTs) and 380 referenced genes relevant for erythropoiesis. The database is organized to provide a cytogenetic band position, a unique name as well as a concise annotation for each entry. Search queries may be performed by name, keyword or cytogenetic location. Search results are linked to primary sequence data and three major human genome browsers for access to information considered current at the time of each search. Hembase provides interested scientists and clinical hematologists with a genome-based approach toward the study of erythroid biology.

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Hepatitis C Virus Databases

Hepatitis C Virus Databases | bioinformatics-databases | Scoop.it

The Hepatitis C Virus (HCV) Database Project was initially funded by the Division of Microbiology and Infectious Diseases of the National Institute of Allergies and Infectious Diseases (NIAID). The HCV database group strives to present HCV-associated, hand-annotated genetic data in a userfriendly way, by providing access to the central database via web-accessible search interfaces and supplying a number of analysis tools.

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Gypsy Database 2.0: database about the evolutionary relationship of viruses, mobile genetic elements (MGEs) and the genomic repeats

Gypsy Database 2.0: database about the evolutionary relationship of viruses, mobile genetic elements (MGEs) and the genomic repeats | bioinformatics-databases | Scoop.it
Welcome to the Gypsy Database (GyDB) an open editable database about the evolutionary relationship of viruses, mobile genetic elements (MGEs) and the genomic repeats where we invite all authors to contribute with their knowledge to improve and expand the topics.

Reference:
Llorens, C., Futami, R., Covelli, L., Dominguez-Escriba, L., Viu, J.M., Tamarit, D., Aguilar-Rodriguez, J. Vicente-Ripolles, M., Fuster, G., Bernet, G.P., Maumus, F., Munoz-Pomer, A., Sempere, J.M., LaTorre, A., Moya, A. (2011) The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0 Nucleic Acids Research (NARESE) 39 (suppl 1): D70-D74 doi: 10.1093/nar/gkq1061
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GWIDD: Genome-wide protein docking database

GWIDD: Genome-wide protein docking database | bioinformatics-databases | Scoop.it

Structural information on interacting proteins is important for understanding life processes at the molecular level. Genome-wide docking database is an integrated resource for structural studies of protein–protein interactions on the genome scale, which combines the available experimental data with models obtained by docking techniques. Current database version (August 2009) contains 25 559 experimental and modeled 3D structures for 771 organisms spanned over the entire universe of life from viruses to humans. Data are organized in a relational database with user-friendly search interface allowing exploration of the database content by a number of parameters. Search results can be interactively previewed and downloaded as PDB-formatted files, along with the information relevant to the specified interactions. The resource is freely available at http://gwidd.bioinformatics.ku.edu

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iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections | bioinformatics-databases | Scoop.it

Gene regulatory networks control developmental, homeostatic, and disease processes by governing precise levels and spatio-temporal patterns of gene expression. Determining their topology can provide mechanistic insight into these processes. Gene regulatory networks consist of interactions between transcription factors and their direct target genes. Each regulatory interaction represents the binding of the transcription factor to a specific DNA binding site near its target gene. Here we present a computational method, called iRegulon, to identify master regulators and direct target genes in a human gene signature, i.e. a set of co-expressed genes. iRegulon relies on the analysis of the regulatory sequences around each gene in the gene set to detect enriched TF motifs or ChIP-seq peaks, using databases of nearly 10.000 TF motifs and 1000 ChIP-seq data sets or “tracks”. Next, it associates enriched motifs and tracks with candidate transcription factors and determines the optimal subset of direct target genes. We validate iRegulon on ENCODE data, and use it in combination with RNA-seq and ChIP-seq data to map a p53 downstream network with new predicted co-factors and targets. iRegulon is available as a Cytoscape plugin, supporting human, mouse, and Drosophila genes, and provides access to hundreds of cancer-related TF-target subnetworks or “regulons”.


Via Mel Melendrez-Vallard
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GreenPhyl - A comparative and functional genomics database for green plants

GreenPhyl - A comparative and functional genomics database for green plants | bioinformatics-databases | Scoop.it

GreenPhylDB is a web resource designed for comparative and functional genomics in plants. The database contains a catalogue of gene families based on gene predictions of genomes, covering a broad taxonomy of green plants. 


Result of our automatic clustering is manually annotated and analyzed by a phylogenetic-based approach to predict homologous relationships. It supports evolution and functional studies to identify candidate gene affecting agronomic traits in crops.

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GPXdb - A Macrophage Expression Database

GPXdb - A Macrophage Expression Database | bioinformatics-databases | Scoop.it

Welcome to the Macrophage Expression Atlas a database for expression profiles of macrophages challenged with a a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults.


Objectives

  • Provide access to quality assessed gene expression datasets
  • Rapid access to gene expression profile macrophage treated with a variety of conditions
  • Provide datasets for Systems biology


Publication [click here]

Grimes GR, Moodie S, Beattie JS, Craigon M, Dickinson P, Forster T, Livingston AD, Mewissen M, Robertson KA, Ross AJ, Sing G and Ghazal P.(2005) GPX-Macrophage Expression Atlas: a database for expression profiles of macrophages challenged with a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults. BMC Genomics. Dec 12;6:178.


  • Integrated Macrophage Biology Group A group bringing together researchers studying macrophage biology in order to derive a consensus for standardising experiments
  • Macrophages A resource for distribution of information about macrophage and osteoclast biology
  • BioLayout Express 3D An application designed for the visualization, clustering and analysis of large network graphs in two and three dimensional space derived primarily, but not exclusively, from biological systems
  • InnateImmunity-SystemsBiology A collaboration to assemble a compendium, or parts list, of the innate immune system with an initial focus on the response of macrophages to Toll-like Receptor (TLR) agonists
  • Siamon Gordon Group Website Information on macrophage biology
  • The European Macrophage and Dendritic Cell Society (EMDS) Society to promote out-standing, innovative studies in the field of macrophage and dendritic cell biology with respect to both basic and clinical research
  • GNF SymAtlas A web-application for published experimental gene functionalization datasets integrated with a searchable gene-centric database of public and proprietary annotations
  • Molecular Interaction Map of Macrophage A large scale molecular interaction map of the macrophage
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RAD - Rice Annotation Database

RAD - Rice Annotation Database | bioinformatics-databases | Scoop.it

RAD is a contig-oriented database for high-quality manual annotation of RGP, which can present non-redundant contig analyses by merging the accumulated PAC/BAC clones.


As of October 2004, the database contains a total of 215 Mb sequence with relevant annotation results (30000 predicted genes.) The database can provide the latest information on manual annotation as well as a comprehensive structural analysis of various features of the rice genome.


Note that the annotation data of chromosomes 1, 3, 4 and 10 are restored from flat files of the public database. These basically contain the predicted genes information but not contain their evidence information.

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GOLD.db: genomics of lipid-associated disorders database

GOLD.db: genomics of lipid-associated disorders database | bioinformatics-databases | Scoop.it


The GOLD.db (Genomics of Lipid-Associated Disorders Database) was developed to address the need for integrating disparate information on the function and properties of genes and their products that are particularly relevant to the biology, diagnosis management, treatment, and prevention of lipid-associated disorders.


Journals * Glossary Meetings * Search Institutions

Database Model Bioinformatics * Microarrays * Databases * Tools

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HbVar - A Database of Human Hemoglobin Variants and Thalassemias

HbVar - A Database of Human Hemoglobin Variants and Thalassemias | bioinformatics-databases | Scoop.it

This is a relational database of information about hemoglobin variants and mutations that cause thalassemia. The initial data came from Syllabi authored by Prof. Titus H.J. Huisman, Mrs. Marianne F.H. Carver, Dr. Erol Baysal, and Prof. Georgi D. Efremov. This information was converted to a database, and now new entries are added and old entries are corrected by our curators, Dr. Henri Wajcman, Dr. George Patrinos, Dr. Kamran Moradkhani, Joseph Borg, and Philippe Joly. HbVar results from a collaboration among several investigators at Penn State University (USA), INSERM Creteil (France), and Boston University Medical Center (USA). Visit our query page or summary page to see the types of information available.

To query on the database, click here.


To access summaries of the categories of the mutations, click here. 
Summaries of mutation categories has counts of the results for common queries and buttons to link to them. 

Most recent update
Difference in mass chart
XPRbase has experimental protocols
FINDbase-related links
    Search FINDbase for beta allele frequencies
    Search FINDbase for alpha allele frequencies
    Search FINDbase for delta allele frequencies
    Note: You may have to install Silverlight software to view the FINDbase pages.
Help Page 
    Help with numbers 
    Help with HGVS nomenclature 
Frequently Asked Questions

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snp :: topoSNP Database

snp :: topoSNP Database | bioinformatics-databases | Scoop.it

Welcome to the topoSNP database. This site produces an interactive visualization of disease and non-disease associated non-synonymous single nucleotide polymorphisms (nsSNPs) and displays geometric and relative entropy calculations.


*** Please note you will need MDL's Chime Plugin to view this page correctly. It can be freely downloaded at http://www.mdlchime.com.***


To start, please select one of the datasets to the right, or enter a protein sequence to BLAST search our database.


Relevant publication TopoSNP, Nucleic Acids Research, 2004

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HERVd - Human Endogenous Retrovirus Database

HERVd - Human Endogenous Retrovirus Database | bioinformatics-databases | Scoop.it

Retroviral genomes or parts of their genomes are present in the DNA of many organisms. Studies of endogenous retroviral nucleotide sequences have become an important part of contemporary retrovirology as well as of molecular and cellular biology and genomics. Human endogenous retroviruses (HERVs) are of special interest also because their expression may be associated with several diseases, including cancer. Various groups of HERVs have been reported in the human genome. Their number can range from one copy to many thousand copies.


This database is compiled from the human genome nucleotide sequences obtained mostly in the Human Genome Projects. We created a relatively simple and fast environment for screening human genome for HERVs. This makes it possible to continuously improve classification and characterization of retroviral families. The HERV database now contains retroviruses from more than 90 % of the human genome.


Start your search by clicking on the Search link below. You can search by HERV families, chromosome positions and several other features. For explanation of abbreviations click on Help. The Fasta search or Blat search are used for comparing your nucleotide sequence against all HERVs in the database. For abbreviations click onHelp. An example of using the database is given below, click Example to check.

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Heme Protein Database

Heme Protein Database | bioinformatics-databases | Scoop.it

The Heme Protein Database couples structural information on a non-redundant set of heme proteins with their associated electrochemical midpoint reduction potential values. The HPD incorporates the structural data on heme proteins in the RCSB Protein Data Bank (PDB) with the protein structure classifications in CATH 3.0.0 and electrochemical data from the primary literature. The data are presented along withMOLMOL images of the heme proteins and links to the Prosthetic Groups and Metal Ions in Protein Active Sites Database, PROMISE

This heme protein structure-function database may be searched in one of the three ways presented at left. The Search by PDB ID feature allows the user to identify the properties of anindividual heme protein. Data on sets of heme proteins can be retrieved using either the Detailed Search Function, which yields a list of all the individual members of the set, or the Global View function, which compiles the data on all the members of the set as a group.

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HDBase - A Huntington's Disease Research Database

HDBase - A Huntington's Disease Research Database | bioinformatics-databases | Scoop.it

Welcome to the future home of HDBase, a community website for Huntington's Disease (HD) research. The purpose of HDBase is to collect and present information that will assist HD researchers in their work.


Content areas that may be covered by the site include the following:

  • Therapeutic studies in mouse, primarily drug screens.
  • HD mouse models with a focus on timelines of disease progression.
  • Antibodies used in HD research.
  • Microarray gene expression studies.
  • Genes and proteins relevant to HD research. This includes HD itself, the growing list of proteins thought to interact directly or indirectly with huntingtin (Htt), and other genes and proteins implicated in the disease process.
  • Molecular pathways thought to be involved in the disease process.
  • Timelines of disease for Mouse models

Presently, we have Y2H and Mass Spec. protein-protein interaction data centered around the HD protein (huntingtin) and information on therapeutic studies in mouse. We also have Human and Mouse Affymetrix Microarray data.

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VarySysDB

VarySysDB | bioinformatics-databases | Scoop.it

VarySysDB

This consists of the following three systems.

Genome Browser
The Generic Genome Browser is a combination of database and interactive Web page for manipulating and displaying annotations on genomes.(gbrowse)
LD Search System
A search system for linkage disequilibrium (LD) bins.
VaryGene 2

This is a system to search, display, and download our research results on human polymorphism based on publicly available data and annotations of transcripts presented by H-InvDB. It provides information about single nucleotide polymorphisms (SNPs), deletion-insertion polymorphisms (DIPs), short tandem repeats (STRs), single amino acid repeats (SARs), structural variation (or copy number variations: CNVs), and their relations to the genome, transcripts, and functional domains.

Functions
Polymorphism
Search this system by features of polymorphism or effects of polymorphism on transcribed products.
Gene
Search this system by H-Inv Transcripts.
STR
Search this system by features of STRs or SARs.
CNV
Search this system by features of CNVs.
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GWIPS - Genome Wide Information on Protein Synthesis Database

GWIPS - Genome Wide Information on Protein Synthesis Database | bioinformatics-databases | Scoop.it

GWIPS-viz aims to provide on-line tools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique, see Ingolia et al (2009) Science.


GWIPS-viz is based on the UCSC Genome Browser, developed by the Genome Informatics Group, Center for Biomolecular Science and Engineering, University of California, Santa Cruz.

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GONUTS: A Gene Ontology Normal Usage Tracking System

GONUTS: A Gene Ontology Normal Usage Tracking System | bioinformatics-databases | Scoop.it

The GONUTS wiki has been set up to provide third-party documentation for users of the Gene Ontology Project. The GO wiki is not an official product of the GO consortium. It was built by users at TAMU for newcomers to the Gene Ontology who want to explore GO usage. The rationale for this wiki is described in About GONUTS.


To browse the ontology pages, search for a term or visit the paramount GO page page and select a branch. For more information about how this wiki is automatically updated, see GO wiki scripts. For Help using the system, see Help:Contents, which is available in the navigation links from all pages.

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Genomic tRNA Database

Genomic tRNA Database | bioinformatics-databases | Scoop.it

This genomic tRNA database contains tRNA gene predictions made by the program tRNAscan-SE (Lowe & Eddy, Nucl Acids Res 25: 955-964, 1997) on complete or nearly complete genomes. Unless otherwise noted, all annotation is automated, and has not been inspected for agreement with published literature.


Inevitably with automated sequence analysis, we find exceptions to general identification rules, isoacceptor type predictions (esp. due to variable post-transcriptional anticodon modification), and questionable tRNA identifications (due to pseudogenes, SINES, or other tRNA-derived elements). We attempt to document all cases we come across, and welcome feedback (lowe @soe.ucsc.edu) on new or unrecognized discrepancies. For a more detailed description of information in tables and the tRNA search algorithm, see the [Legend]. 


[Find tRNAs]

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rougeforfire's curator insight, March 26, 2014 6:15 AM

Searching for a #transcripts #database ?? why not this one ?

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greengenes.lbl.gov - Aligned 16S rDNA data and tools

greengenes.lbl.gov - Aligned 16S rDNA data and tools | bioinformatics-databases | Scoop.it

The most recent Greengenes database and taxonomy updates are now found at greengenes.secondgenome.com. Taxonomic information on this site is deprecated and should be used with caution. 


The greengenes web application provides access to the 2011 version of the greengenes 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading.  The data and tools presented by greengenes can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences.  If you are an ARB user, you can use greengenes to keep your own local database current.

      • Search is now possible using new Simrank (developed by Niels Larsen) for similarity searching against the 2011 greengenes sequences.
      • New import filter template posted for slurping greengenes exports into ARB.
      • Looking for Hugenholtz or PHPR taxonomy? It is now the greengenes taxonomy.
      • Dr. Mike Dyall-Smith has graciously made available his tutorial for installing Arb on MacOSX. Thanks Mike.
      • The greengenes taxonomy for the Cyanobacteria is now consistent with cyanoDB using cyanoDB type species as a guide to map cyanoDB taxonomy to the greengenes reference 16S tree.
      • Thanks to Greg Caporaso and Rob Knight for posting OTU reference and utility files for use with QIIME software.
      • The Wall Street Journal picks the Berkeley PhyloChip as the top advance in environmental technology of 2008 and 3rd best innovation overall.
      • Pollution Engineering Magazine selects Berkeley PhyloChip as most likely to aid pollution control and abatement in the near future.
      • The Berkeley PhyloChip wins R&D100 award as one of the 100 most significant technological advances of the year.
      • Are you the world expert on the taxonomy of a particular phylogenetic lineage? Have you checked this database and nobody has got it right? Tell us! - we will fix it.

    We thank Jakob Fredslund for developing a tool, Gexcellent - to convert XML trees to Newick format!

    We thank J.P. Euzéby and Hans Trüper for expert etymological advice.
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    eSLDB - Eukaryotic Subcellular Localization Database

    eSLDB - Eukaryotic Subcellular Localization Database | bioinformatics-databases | Scoop.it

    eSLDB is a database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions.

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    Kidhome - The Kidney Development Database

    Kidhome - The Kidney Development Database | bioinformatics-databases | Scoop.it
    Reading Material
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    GOBASE - The Organelle Genome Database

    GOBASE - The Organelle Genome Database | bioinformatics-databases | Scoop.it

    GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts. GOBASE is currently expanding to include information on representative bacteria that are thought to be specifically related to the bacterial ancestors of mitochondria and chloroplasts.


    The current version of GOBASE, release 25, is based on GenBank release 175 and was released in June 2010. This release includes 177,000 new mitochondrial sequences and 41,000 new chloroplast sequences.

    Unfortunately, funding for GOBASE has expired, so this will be the last update. Maintenance of GOBASE will cease at the end of August 2010 and the contact address gobase@bch.umontreal.ca will also become defunct at this time.


    Users are requested to cite GOBASE in any publication making use of GOBASE data. The preferred reference is:

    GOBASE - an organelle genome database

    O'Brien, Emmet A., Zhang, Yue, Wang, Eric, Marie, Veronique, Badejoko, Wole, Lang, B. Franz and Burger, Gertraud.
    Nucleic Acids Res. 37:D946-950 (2009)


    Full text available here


    [ OGMP | FMGP | GOBASE | PID | CIAR-PEB | ISEP | Entrez | Blast | Analysis | Resources | Organelle genomes ]

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    dbERGE II - a database of experimental results on gene expression

    dbERGE II - a database of experimental results on gene expression | bioinformatics-databases | Scoop.it

    dbERGE II stores experiment and result details for various types of experiments. The current types of experiments available are:

    1. DNA transfer experiments (Transfections and Transgenic mice) 
    2. Binding assays (Gel shift, In-vivo footprint, In-vitro footprint and Methylation interference) 
    3. Hypersensitive sites 
    4. ChIP - on - chip experiments

    Explanation of each experiment type is given here.


    Help and Documentation
    Instructions for query page
    Key for the query page's graphical display
    Database schema diagrams
    Frequently asked questions
    How to contact us


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