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on page 1 showing 9 out of 9 results

Cite this (Animal QTLdb, RRID:SCR_001748)

URL: http://www.animalgenome.org/cgi-bin/QTLdb/index

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Database of publicly available trait mapping data, i.e. QTL (phenotype / expression, eQTL), candidate gene and association data (GWAS) and copy number variations (CNV) mapped to livestock animal genomes, to facilitate locating and comparing discoveries within and between species. New data and database tools are continually developed to align various trait mapping data to map-based genome features, such as annotated genes. Besides the QTL data from species listed, the QTLdb is open to house QTL/association date from other animal species where feasible. Most scientific journals require that any original QTL/association data be deposited into a public databases before a paper may be accepted for publication. User curator accounts are provided for direct data deposit. By searching or browsing the QTLdb, one can: # Find all QTL on one chromosome
# Find all chromosomes that bear QTL for the same trait
# List all QTL from a particular publication
# Find all markers underlining a QTL
# Find DNA sequences associated with certain markers
# Use LocusLink to further search for candidate genes by comparative maps
# Find experiment details in brief for a given publication
# Find all parameters describing a QTL, as well as test statistics
Users can download the QTLdb data from each species or individual chromosome.

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    ASAP

Cite this (ASAP, RRID:SCR_001849)

URL: https://omictools.com/asap-3-tool

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Database and web interface developed to store, update and distribute genome sequence data and gene expression data. 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. Use of some of this preliminary data is conditional, and it is the users responsibility to read the data release policy and to verify that any use of specific data obtained through ASAP is consistent with this policy. There are four main routes to viewing the information in ASAP: # a summary page, # a form to query the genome annotations, # a form to query strain collections, and # a form to query the experimental data. Navigational buttons appear on every page allowing users to jump to any of these four points.

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    BeeBase

Cite this (BeeBase, RRID:SCR_008966)

URL: http://hymenopteragenome.org/beebase/

Resource Type: Resource, data analysis service, production service resource, analysis service resource, data set, service resource, data or information resource

Gene sequences and genomes of Bombus terrestris, Bombus impatiens, Apis mellifera and three of its pathogens, that are discoverable and analyzed via genome browsers, blast search, and apollo annotation tool. The genomes of two additional species, Apis dorsata and A. florea are currently under analysis and will soon be incorporated.

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Cite this (Fungal Genome Initiative, RRID:SCR_003169)

URL: http://www.broad.mit.edu/annotation/fungi/fgi/

Resource Type: Resource, data set, data or information resource

Produces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. The FGI is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers the value of data from each organism, given their role in basic research, health, agriculture and industry, as well as their value in comparative genomics.

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    Gramene

Cite this (Gramene, RRID:SCR_002829)

URL: http://www.gramene.org

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

A curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site.

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Cite this (Magnaporthe comparative Database, RRID:SCR_003079)

URL: http://www.broadinstitute.org/annotation/genome/magnaporthe_comparative/MultiHome.html

Resource Type: Resource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resource

The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae. It provides users the tools to BLAST search, browse genome regions (to retrieve DNA, find clones, and graphically view sequence regions), and provides gene indexes and genome statistics. We were funded to attempt 7x sequence coverage comprising paired end reads from plasmids, Fosmids and BACs. Our strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated and reassembled. Our specific aims are as follows: 1. Generate and assemble sequence reads yielding 7X coverage of the Magnaporthe oryzae genome through whole genome shotgun sequencing. 2. Generate and incorporate BAC and Fosmid end sequences into the genome assembly to provide a paired-end of average every 2 kb. 3. Integrate the genome sequence with existing physical and genetic map information. 4. Perform automated annotation of the sequence assembly. 5. Distribute the sequence assembly and results of our annotation and analysis through a freely accessible, public web server and by deposition of the sequence assembly in GenBank.

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    MaizeGDB

Cite this (MaizeGDB, RRID:SCR_006600)

URL: http://www.maizegdb.org

Resource Type: Resource, topical portal, database, analysis service resource, organism-related portal, data analysis service, service resource, portal, production service resource, storage service resource, data repository, data or information resource

Collection of data related to crop plant and model organism Zea mays. Used to synthesize, display, and provide access to maize genomics and genetics data, prioritizing mutant and phenotype data and tools, structural and genetic map sets, and gene models and to provide support services to the community of maize researchers. Data stored at MaizeGDB was inherited from the MaizeDB and ZmDB projects. Sequence data are from GenBank. Data are searchable by phenotype, traits, Pests, Gel Pattern, and Mutant Images.

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Cite this (NAGRP Bioinformatics Coordination Program, RRID:SCR_006564)

URL: http://www.animalgenome.org/

Resource Type: Resource, topical portal, service resource, portal, data or information resource

We at NRSP-8 bioinformatics coordination program strive to serve the animal genomics research community to better use computer tools and methods, to best utilize available resources, and in working with researchers in the community, to effectively share, combine, manage, manipulate, and analyze information from genomics/genetics studies. This site is designed as an information center to serve the national animal genome research projects of cattle, chicken, pigs, sheep, horse, and aquaculture species. This is home to databases and web sites (being) built for structural, functional and application oriented studies of the animal genomics, to serve the purpose of research, education and related activities in the scientific, industrial and educational communities in the states and world wide. The challenges in bioinformatics support/research for animal genomics may involve * Effective data collection, organization and management * Rapid development of most needed bioinformatics tools and resources * Efficient use of these tools for innovative data analysis Projects: * Animal Trait Ontology (ATO) Project * Virtual Comparative Genomics * The Past, the Current, and the Potentials * Collaborative and Hosted Works

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Cite this (PLEXdb - Plant Expression Database, RRID:SCR_006963)

URL: http://www.plexdb.org/index.php

Resource Type: Resource, topical portal, database, analysis service resource, production service resource, data analysis service, service resource, portal, storage service resource, data repository, data or information resource

PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data. The integrated tools of PLEXdb allow investigators to use commonalities in plant biology for a comparative approach to functional genomics through use of large-scale expression profiling data sets.

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