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Found 27 result(s)

Autism Chromosome Rearrangement Database

ACRD

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The Autism Chromosome Rearrangement Database is a collection of hand curated breakpoints and other genomic features, related to autism, taken from publicly available literature: databases and unpublished data. The database is continuously updated with information from in-house experimental data as well as data from published research studies.

OrthoMCL

Ortholog Groups of Protein Sequences

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OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. It provides not only groups shared by two or more species/genomes, but also groups representing species-specific gene expansion families. So it serves as an important utility for automated eukaryotic genome annotation. OrthoMCL starts with reciprocal best hits within each genome as potential in-paralog/recent paralog pairs and reciprocal best hits across any two genomes as potential ortholog pairs. Related proteins are interlinked in a similarity graph. Then MCL (Markov Clustering algorithm,Van Dongen 2000; www.micans.org/mcl) is invoked to split mega-clusters. This process is analogous to the manual review in COG construction. MCL clustering is based on weights between each pair of proteins, so to correct for differences in evolutionary distance the weights are normalized before running MCL.

FungiDB

The Fungal and Oomycete Genomics Resource

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FungiDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for the kingdom Fungi. FungiDB was first released in early 2011 as a collaborative project between EuPathDB and the group of Jason Stajich (University of California, Riverside). At the end of 2015, FungiDB was integrated into the EuPathDB bioinformatic resource center. FungiDB integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes comparative genomics, analysis of gene expression, and supplemental bioinformatics analyses and a web interface for data-mining.

FlyReactome

a curated knowledgebase of drosophila melanogaster pathways

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<<<!!!<<< This repository is no longer available. This record is out dated >>>!!!>>>- eir fields, maintained by the FlyReactome staff.

Metlin

The original and most comprehensive MS/MS metabolite database

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METLIN represents the largest MS/MS collection of data with the database generated at multiple collision energies and in positive and negative ionization modes. The data is generated on multiple instrument types including SCIEX, Agilent, Bruker and Waters QTOF mass spectrometers.

heidICON

Die Heidelberger Bilddatenbank

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heidICON is provided by Heidelberg University Library and is the "Virtual Slide Collection" in progress of organization of Heidelberg University. In addition to record graphic material on current interest for research and teaching, the University departments and institutes can digitize and transfer their already existing slide collections.

Cancer GenomeAtlas Data Portal

Cancer Genome Atlas Data Portal

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The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The Data Coordinating Center (DCC) is the central provider of TCGA data. The DCC standardizes data formats and validates submitted data.

circbase

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Thousands of circular RNAs (circRNAs) have recently been shown to be expressed in eukaryotic cells [Salzman et al. 2012, Jeck et al. 2013, Memczak et al. 2013, Salzman et al. 2013]. Here you can explore public circRNA datasets and download the custom python scripts needed to discover circRNAs in your own (ribominus) RNA-seq data.

Hardwood Genomics Project

HWG

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This database serves forest tree scientists by providing online access to hardwood tree genomic and genetic data, including assembled reference genomes, transcriptomes, and genetic mapping information. The web site also provides access to tools for mining and visualization of these data sets, including BLAST for comparing sequences, Jbrowse for browsing genomes, Apollo for community annotation and Expression Analysis to build gene expression heatmaps.

Cystic Fibrosis Mutation Database

CFTR1

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The Cystic Fibrosis Mutation Database (CFTR1) was initiated by the Cystic Fibrosis Genetic Analysis Consortium in 1989 to increase and facilitate communications among CF researchers, and is maintained by the Cystic Fibrosis Centre at the Hospital for Sick Children in Toronto. The specific aim of the database is to provide up to date information about individual mutations in the CFTR gene. In a major upgrade in 2010, all known CFTR mutations and sequence variants have been converted to the standard nomenclature recommended by the Human Genome Variation Society.

GiardiaDB

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Giardia lamblia is a significant, environmentally transmitted, human pathogen and an amitochondriate protist. It is a major contributor to the enormous worldwide burden of human diarrheal diseases, yet the basic biology of this parasite is not well understood. No virulence factor has been identified. The Giardia lamblia genome contains only 12 million base pairs distributed onto five chromosomes. Its analysis promises to provide insights about the origins of nuclear genome organization, the metabolic pathways used by parasitic protists, and the cellular biology of host interaction and avoidance of host immune systems. Since the divergence of Giardia lamblia lies close to the transition between eukaryotes and prokaryotes in universal ribosomal RNA phylogenies, it is a valuable, if not unique, model for gaining basic insights into genetic innovations that led to formation of eukaryotic cells. In evolutionary terms, the divergence of this organism is at least twice as ancient as the common ancestor for yeast and man. A detailed study of its genome will provide insights into an early evolutionary stage of eukaryotic chromosome organization as well as other aspects of the prokaryotic / eukaryotic divergence.

NCBI Probe

Probe

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<<<!!!<<< NCBI has retired the Probe Database >>>!!!>>>

RCSB Protein Data Bank

RCSB PDB

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The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids. These are the molecules of life that are found in all organisms including bacteria, yeast, plants, flies, other animals, and humans. Understanding the shape of a molecule helps to understand how it works. This knowledge can be used to help deduce a structure's role in human health and disease, and in drug development. The structures in the archive range from tiny proteins and bits of DNA to complex molecular machines like the ribosome.

Fungal Genetics Stock Center

FGSC

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The Fungal Genetics Stock Center has preserved and distributed strains of genetically characterized fungi since 1960. The collection includes over 20,000 accessioned strains of classical and genetically engineered mutants of key model, human, and plant pathogenic fungi. These materials are distributed as living stocks to researchers around the world.

The Human Protein Atlas

HPA

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The Swedish Human Protein Atlas project has been set up to allow for a systematic exploration of the human proteome using Antibody-Based Proteomics. This is accomplished by combining high-throughput generation of affinity-purified antibodies with protein profiling in a multitude of tissues and cells assembled in tissue microarrays. Confocal microscopy analysis using human cell lines is performed for more detailed protein localization. The program hosts the Human Protein Atlas portal with expression profiles of human proteins in tissues and cells. The main objective of the resource centre is to produce specific antibodies to human target proteins using a high-throughput production method involving the cloning and protein expression of Protein Epitope Signature Tags (PrESTs). After purification, the antibodies are used to study expression profiles in cells and tissues and for functional analysis of the corresponding proteins in a wide range of platforms.

IUCN Red List of Threatened Species

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The IUCN Red List of Threatened Species provides taxonomic, conservation status and distribution data on plants and animals that are critically endangered, endangered and vulnerable. Data are available in Esri File Geodatabase format, Esri Shapefile format, and Excel format.

Canadian Poisonous Plants Information System

Système canadien d'information sur les plantes toxiques

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!!! <<< the repository is offline >>> !!! The Canadian Poisonous Plants Information System presents data on plants that cause poisoning in livestock, pets, and humans. The plants include native, introduced, and cultivated outdoor plants as well as indoor plants that are found in Canada. Some food and herbal plants that may cause potential poisoning problems are also included.

STITCH 4.0

Search Tool for Interactions of Chemicals

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The Database explores the interactions of chemicals and proteins. It integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins.

VEuPathDB

formerly: Eukaryotic Pathogen Database Resources

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EuPathDB (formerly ApiDB) is an integrated database covering the eukaryotic pathogens in the genera Acanthamoeba, Annacaliia, Babesia, Crithidia, Cryptosporidium, Edhazardia, Eimeria, Encephalitozoon, Endotrypanum, Entamoeba, Enterocytozoon, Giardia, Gregarina, Hamiltosporidium, Leishmania, Nematocida, Neospora, Nosema, Plasmodium, Theileria, Toxoplasma, Trichomonas, Trypanosoma and Vavraia, Vittaforma). While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all of these resources, and the opportunity to leverage orthology for searches across genera.

PlasmoDB

Plasmodium Genomics Resource

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PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria.

World Register of Marine Species

WoRMS

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The World Register of Marine Species (WoRMS) integrates approximately 100 marine datbases to provide an authoritative and comprehensive list of marine organisms. WoRMS has an editorial system where taxonomic groups are managed by experts responsible for the quality of the information. WorMS register of marine species emerged from the European Register of Marine Species (ERMS) and the Flanders Marine Institute (VLIZ). WoRMS is a contribution to Lifewatch, Catalogue of Life, Encyclopedia of Life, Global Biodiversity Information Facility and the Census of Marine Life.

1000 Genomes

Thousand Genomes

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The 1000 Genomes Project is an international collaboration to produce an extensive public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts. This resource will support genome-wide association studies and other medical research studies. The genomes of about 2500 unidentified people from about 25 populations around the world will be sequenced using next-generation sequencing technologies. The results of the study will be freely and publicly accessible to researchers worldwide. The International Genome Sample Resource (IGSR) has been established at EMBL-EBI to continue supporting data generated by the 1000 Genomes Project, supplemented with new data and new analysis.

INTEGRALL

The Integron Database

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INTEGRALL is a web-based platform dedicated to compile information on integrons and designed to organize all the data available for these genetic structures. INTEGRALL provides a public genetic repository for sequence data and nomenclature and offers to scientists an easy and interactive access to integron's DNA sequences, their molecular arrangements as well as their genetic contexts.

TwinsUK

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The TwinsUK resource is the biggest UK adult twin registry of 14.000 twins used to study the genetic and environmental aetiology of age related complex traits and diseases.

Pseudomonas Genome DB

Pseudomonas Genome Database

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The Pseudomonas Genome Database collaborates with an international panel of expert Pseudomonas researchers to provide high quality updates to the PAO1 genome annotation and make cutting edge genome analysis data available.