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Found 56 result(s)

NCBI Influenza Virus Resource

NCBI Flu

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This resource allows users to search for and compare influenza virus genomes and gene sequences taken from GenBank. It also provides a virus sequence annotation tool and links to other influenza resources: NIAID project, JCVI Flu, Influenza research database, CDC Flu, Vaccine Selection and WHO Flu. NOTE: The redirects that are planned for completion by May 2024 will NOT impact the Influenza Virus Resource in any way. The Influenza Virus Resource will continue to be available, serving up data to support our Flu-research community.

NCBI Protein Clusters

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The Entrez Protein Clusters database contains annotation information, publications, structures and analysis tools for related protein sequences encoded by complete genomes. The data available in the Protein Clusters Database is generated from prokaryotic genomic studies and is intended to assist researchers studying micro-organism evolution as well as other biological sciences. Available genomes include plants and viruses as well as organelles and microbial genomes.

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.

ASAP

A systematic annotation package for community analysis of genomes

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ASAP (a systematic annotation package for community analysis of genomes) is a relational database and web interface developed to store, update and distribute genome sequence data and gene expression data collected by or in collaboration with researchers at the University of Wisconsin - Madison. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments.

NCBI Genome

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<<<!!!<<< Effective May 2024, NCBI's Genome resource will no longer be available. NCBI Genome data can now be found on the NCBI Datasets taxonomy pages. https://www.re3data.org/repository/r3d100014298 >>>!!!>>> The Genome database contains annotations and analysis of eukaryotic and prokaryotic genomes, as well as tools that allow users to compare genomes and gene sequences from humans, microbes, plants, viruses and organelles. Users can browse by organism, and view genome maps and protein clusters.

VectorBase

Bioinformatics Resource for Invertebrate Vectors of Human Pathogens

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VectorBase provides data on arthropod vectors of human pathogens. Sequence data, gene expression data, images, population data, and insecticide resistance data for arthropod vectors are available for download. VectorBase also offers genome browser, gene expression and microarray repository, and BLAST searches for all VectorBase genomes. VectorBase Genomes include Aedes aegypti, Anopheles gambiae, Culex quinquefasciatus, Ixodes scapularis, Pediculus humanus, Rhodnius prolixus. VectorBase is one the Bioinformatics Resource Centers (BRC) projects which is funded by National Institute of Allergy and Infectious Diseases (NAID).

Estonian Biocentre Free Data

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A small genotype data repository containing data used in recent papers from the Estonian Biocentre. Most of the data pertains to human population genetics. PDF files of the papers are also freely available.

PhytoPath

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<<<!!!<<< This site is no longer maintained and is provided for reference only. Some functionality or links may not work. For all enquiries please contact the Ensembl Helpdesk http://www.ensembl.org/Help/Contact >>>!!!>>> PhytoPath is a new bioinformatics resource that integrates genome-scale data from important plant pathogen species with literature-curated information about the phenotypes of host infection. Using the Ensembl Genomes browser, it provides access to complete genome assembly and gene models of priority crop and model-fungal, oomycete and bacterial phytopathogens. PhytoPath also links genes to disease progression using data from the curated PHI-base resource. PhytoPath portal is a joint project bringing together Ensembl Genomes with PHI-base, a community-curated resource describing the role of genes in pathogenic infection. PhytoPath provides access to genomic and phentoypic data from fungal and oomycete plant pathogens, and has enabled a considerable increase in the coverage of phytopathogen genomes in Ensembl Fungi and Ensembl Protists. PhytoPath also provides enhanced searching of the PHI-base resource as well as the fungi and protists in Ensembl Genomes.

NCBI Virus Variation

Influenza Virus Database

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<<<!!!<<< Effective May 2024, Virus Variation will no longer be available and will be redirected to NCBI Virus https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/ >>>!!!>>> NCBI Virus Variation is a specialized database which collects tools to provide searchable resources in the fields of Influenza virus, Dengue virus, and West Nile virus. Specific BLAST databases are listed. Their new publications are also available in their site. Rotavirus database will be added in their site soon.

AmoebaDB

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AmoebaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. In its first iteration (released in early 2010), AmoebaDB contains the genomes of three Entamoeba species (see below). AmoebaDB integrates whole genome sequence and annotation and will rapidly expand to include experimental data and environmental isolate sequences provided by community researchers . The database includes supplemental bioinformatics analyses and a web interface for data-mining.

NCBI Datasets

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NCBI Datasets is a continually evolving platform designed to provide easy and intuitive access to NCBI’s sequence data and metadata. NCBI Datasets is part of the NIH Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.

OrtholugeDB

The Ortholog Database

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OrtholugeDB contains Ortholuge-based orthology predictions for completely sequenced bacterial and archaeal genomes. It is also a resource for reciprocal best BLAST-based ortholog predictions, in-paralog predictions (recently duplicated genes) and ortholog groups in Bacteria and Archaea. The Ortholuge method improves the specificity of high-throughput orthology prediction.

Wellcome Trust Sanger Institute, Scientific resources

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The Wellcome Trust Sanger Institute is a charitably funded genomic research centre located in Hinxton, nine miles south of Cambridge in the UK. We study diseases that have an impact on health globally by investigating genomes. Building on our past achievements and based on priorities that exploit the unique expertise of our Faculty of researchers, we will lead global efforts to understand the biology of genomes. We are convinced of the importance of making this research available and accessible for all audiences. reduce global health burdens.

SARS-CoV-2 Data Hub

SARS-CoV

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This Web resource provides data and information relevant to SARS coronavirus. It includes links to the most recent sequence data and publications, to other SARS related resources, and a pre-computed alignment of genome sequences from various isolates. In order to provide free and easy access to genome and protein sequences and associated metadata from the SARS-CoV-2, we created a dedicated Severe acute respiratory syndrome coronavirus 2 data hub. You can access the Results Table on SARS-CoV-2 data hub, by pressing "RefSeq genomes", "nucleotide" or "protein" links on announcement banner located on NCBI home page, in "Find data" navigation menu or using "Up-to-date SARS-CoV-2" shortcut button in "Search by virus" form. SARS-CoV-2 sequences is part of NCBI Virus https://www.re3data.org/repository/r3d100014322

Follicular Lymphoma Genome Data at Canada's Michael Smith Genome Sciences Centre (BCGSC)

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<<<!!!<<< Genome data generated by BC Genome Sciences Centre is no longer available through this site as it is regularly deposited into controlled data repositories such as the European Genome Phenome Archive (EGA); ICGC (International Cancer Genome Consortium) and the Genome Data Commons (GDC) >>>!!!>>> Mapping, copy number analysis, sequence and gene expression data generated by the High Resolution Analysis of Follicular Lymphoma Genomes project. The data will be available for 24 patients with follicular lymphoma. All data will be made as widely and freely available as possible while safeguarding the privacy of participants, and protecting confidential and proprietary data.The data from this project will be submitted to public genomic data sources. These sources will be listed on this web site as the data becomes available in these external data sources.

Ensembl Genomes

e!EnsemblGenomes

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The Ensembl genome annotation system, developed jointly by the EBI and the Wellcome Trust Sanger Institute, has been used for the annotation, analysis and display of vertebrate genomes since 2000. Since 2009, the Ensembl site has been complemented by the creation of five new sites, for bacteria, protists, fungi, plants and invertebrate metazoa, enabling users to use a single collection of (interactive and programatic) interfaces for accessing and comparing genome-scale data from species of scientific interest from across the taxonomy. In each domain, we aim to bring the integrative power of Ensembl tools for comparative analysis, data mining and visualisation across genomes of scientific interest, working in collaboration with scientific communities to improve and deepen genome annotation and interpretation.

Ensembl Bacteria

e!EnsemblBacteria

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This site provides access to complete, annotated genomes from bacteria and archaea (present in the European Nucleotide Archive) through the Ensembl graphical user interface (genome browser). Ensembl Bacteria contains genomes from annotated INSDC records that are loaded into Ensembl multi-species databases, using the INSDC annotation import pipeline.

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.

KBase

KBase: The U.S. Department of Energy Systems Biology Knowledgebase

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The Department of Energy Systems Biology Knowledgebase (KBase) is a software and data platform designed to meet the grand challenge of systems biology: predicting and designing biological function. KBase integrates data and tools in a unified graphical interface so users do not need to access them from numerous sources or learn multiple systems in order to create and run sophisticated systems biology workflows. Users can perform large-scale analyses and combine multiple lines of evidence to model plant and microbial physiology and community dynamics. KBase is the first large-scale bioinformatics system that enables users to upload their own data, analyze it (along with collaborator and public data), build increasingly realistic models, and share and publish their workflows and conclusions. KBase aims to provide a knowledgebase: an integrated environment where knowledge and insights are created and multiplied.

eHOMD

expanded Human Oral Microbiome Database

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The goal of creating the Human Oral Microbiome Database (HOMD) is to provide the scientific community with comprehensive information o­n the approximately 700 prokaryote species that are present in the human oral cavity. Approximately 49% are officially named, 17% unnamed (but cultivated) and 34% are known o­nly as uncultivated phylotypes. The HOMD presents a provisional naming scheme for the currently unnamed species so that strain, clone, and probe data from any laboratory can be directly linked to a stably named reference scheme. The HOMD links sequence data with phenotypic, phylogenetic, clinical, and bibliographic information. Genome sequences for oral bacteria determined as part of this project, the Human Microbiome Project, and other sequencing projects are being added to the HOMD as they become available. Genomes for 315 oral taxa (46% of taxa o­n HOMD) are currently available o­n HOMD. The HOMD site offers easy to use tools for viewing all publically available oral bacterial genomes.

ExPASy Bioinformatics Resource Portal

SIB Bioinformatics Resource Portal

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Swiss Institute of Bioinformatics (SIB) coordinates research and education in bioinformatics throughout Switzerland and provides bioinformatics services to the national and international research community. ExPASy gives access to numerous repositories and databases of SIB. For example: array map, MetaNetX, SWISS-MODEL and World-2DPAGE, and many others see a list here http://www.expasy.org/resources

DEG

Database of Essential Genes

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DEG hosts records of currently available essential genomic elements, such as protein-coding genes and non-coding RNAs, among bacteria, archaea and eukaryotes. Essential genes in a bacterium constitute a minimal genome, forming a set of functional modules, which play key roles in the emerging field, synthetic biology.

Fungal Mitochondrial Genome Project

FMGP

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The goals of FMGP are to: (i) sequence complete mitochondrial genomes from all major fungal lineages, (ii) infer a robust fungal phylogeny, (iii) define the origin of the fungi, their protistan ancestors, and their specific phylogenetic link to the animals, (iv) investigate mitochondrial gene expression, introns, RNAse P RNA structures, mobile elements.

Viral Bioinformatics Resource Center

VBRC

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Databases of viral genomic information (genes, gene families, and genomes), and software to perform comparative genomics analyses

Genomes OnLine Database

GOLD

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GOLD is currently the largest repository for genome project information world-wide. The accurate and efficient genome project tracking is a vital criterion for launching new genome sequencing projects, and for avoiding significant overlap between various sequencing efforts and centers.