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Non-human variation databases | Genome variant analysis

Gramene
Dataset

Gramene

Offers comparative functional genomics in crops and model plant species.…

Offers comparative functional genomics in crops and model plant species. Gramene uses information generated from projects supported by public funds to improve the study of cross-species comparisons.…

FlySNP
Dataset

FlySNP

Aims to provide the information and technical resources to support…

Aims to provide the information and technical resources to support high-throughput positional cloning in Drosophila melanogaster. These resources include a high-density genome-wide map of single…

IMSR
Dataset

IMSR International Mouse Strain Resource

Provides an online searchable web-based catalog of mouse resources, including…

Provides an online searchable web-based catalog of mouse resources, including inbred, mutant, and genetically engineered mice, cryopreserved embryos and gametes, and embryonic stem (ES) cell lines.…

SoyKB
Dataset

SoyKB Soybean Knowledge Base

A comprehensive web resource developed for bridging soybean translational…

A comprehensive web resource developed for bridging soybean translational genomics and molecular breeding research. It provides information for six entities including genes/proteins, microRNAs/sRNAs,…

TBDB
Dataset

TBDB TuBerculosis DataBase

An online database providing integrated access to genome sequence, expression…

An online database providing integrated access to genome sequence, expression data and literature curation for tuberculosis (TB). TBDB currently houses genome assemblies for numerous strains of…

CeNDR
Dataset

CeNDR C. elegans Natural Diversity Resource

A platform to enable statistical genetics and genomics studies of…

A platform to enable statistical genetics and genomics studies of Caenorhabditis elegans and to connect the results to human disease. CeNDR provides the research community with wild strains,…

Panzea
Dataset

Panzea

The public web site of the Molecular and Functional Diversity in the Maize…

The public web site of the Molecular and Functional Diversity in the Maize Genome project. Panzea provides access to the genotype, phenotype and polymorphism data produced by the project through…

AutoSNPdb
Dataset

AutoSNPdb

Integrates SNP and gene annotation information with a graphical viewer.…

Integrates SNP and gene annotation information with a graphical viewer. AutoSNPdb hosts data for the important crops rice, barley and Brassica. Users may rapidly identify polymorphic sequences of…

GABI-Kat…
Dataset

GABI-Kat SimpleSearch

A Flanking Sequence Tag (FST)-based database for T-DNA insertion mutants…

A Flanking Sequence Tag (FST)-based database for T-DNA insertion mutants generated by the GABI-Kat project.

TOMATOMICS
Dataset

TOMATOMICS

Provides an access to the information on the cDNA clone resources, full-length…

Provides an access to the information on the cDNA clone resources, full-length mRNA sequences, gene structures, expression profiles and functional annotations of genes of Solanum lycopersicum…

MDS_IES_DB
Dataset

MDS_IES_DB

A dynamic database featuring ciliate genome rearrangement annotations that…

A dynamic database featuring ciliate genome rearrangement annotations that include macronuclear destined segment, internal eliminated segment, and pointer annotations. MDS_IES_DB provides tools for…

ISVdb
Dataset

ISVdb Inbred Strain Variant Database

Provides information about collaborative cross (CC) sequence. ISVdb is a…

Provides information about collaborative cross (CC) sequence. ISVdb is a database that offers users a list of probabilistic genotype and diplotype data. It also includes different functions such as:…

WormQTL
Dataset

WormQTL

Public archive and analysis web portal for natural variation data in…

Public archive and analysis web portal for natural variation data in Caenorhabditis spp.

ChickVD
Dataset

ChickVD Chicken Variation Database

An integrated information system for the storage, retrieval, visualization and…

An integrated information system for the storage, retrieval, visualization and analysis of chicken DNA sequence variation. To enhance the discovery of relationships between sequence variation and…

DPDB
Dataset

DPDB Drosophila Polymorphism DataBase

A secondary database that provides a collection of all well-annotated…

A secondary database that provides a collection of all well-annotated polymorphic sequences in Drosophila together with their associated diversity measures and options for reanalysis of the data that…

RVD
Dataset

RVD Rice Variation Database

A rice knowledgebase to achieve data integration through community-contributed…

A rice knowledgebase to achieve data integration through community-contributed modules. IC4R provides a reference genome with standardized and accurates gene annotations based on huge amounts of…

IC4R
Dataset

IC4R Information Commons for Rice

Gathers information about rice. IC4R provides a reference genome with…

Gathers information about rice. IC4R provides a reference genome with standardized and accurate gene annotations based on huge amounts of omics data and large quantities of rice-related literatures.…

Rice SNP-Seek…
Dataset

Rice SNP-Seek Database

Provides genotype, phenotype, and variety information for rice. The Rice…

Provides genotype, phenotype, and variety information for rice. The Rice SNP-Seek Database allows to quickly retrieve single-nucleotide polymorphism (SNP) alleles for all varieties in a genome…

MiSNPDb
Dataset

MiSNPDb Mangnifera Indica Single Nucleotide Polymorphism DataBase

Provides molecular markers with genome information and single nucleotide…

Provides molecular markers with genome information and single nucleotide polymorphism (SNP) data for mango. MiSNPDb has customized advance search options for haplotypes, depth and the varieties…

Zfishbook
Dataset

Zfishbook

Provides a real-time database with full and unrestricted access to all…

Provides a real-time database with full and unrestricted access to all information. The zfishbook site is designed to be a multiuser and dynamic database. It represents a central hub for molecular,…

SorGSD
Dataset

SorGSD Sorghum Genome SNP Database

A sorghum genome SNP database. SorGSD covers a diverse collection of 48 sorghum…

A sorghum genome SNP database. SorGSD covers a diverse collection of 48 sorghum lines that fall into four groups, viz., improved varieties, landraces, wild and weedy sorghums, and a wild relative…

DoGSD
Dataset

DoGSD Dog Genome SNP Database

A data container for the variation information of dog/wolf genomes. DoGSD was…

A data container for the variation information of dog/wolf genomes. DoGSD was designed and constructed as a SNPs detector and visualization tool to provide the research community a useful resource…

RiceVarMap
Dataset

RiceVarMap Rice Variation Map

A database of rice genomic variations. The database provides comprehensive…

A database of rice genomic variations. The database provides comprehensive information of 6,551,358 single nucleotide polymorphisms (SNPs) and 1,214,627 insertions/deletions (INDELs) identified from…

DNApod
Dataset

DNApod

Provides genome-wide DNA polymorphisms of plants, with crop plants being the…

Provides genome-wide DNA polymorphisms of plants, with crop plants being the top priority. DNApod is an integrated database of genome-wide DNA polymorphisms detected under uniform analytical…

MamPol
Dataset

MamPol

Stores all the polymorphic sequences for the Mammalia class. MamPol contains…

Stores all the polymorphic sequences for the Mammalia class. MamPol contains polymorphism data, including both nucleotide sequences and their associated diversity estimates. The database provides…

PigGIS
Dataset

PigGIS Pig Genomic Informatics System

Furnishes pig gene annotations in all sequenced genomic regions. PigGIS gathers…

Furnishes pig gene annotations in all sequenced genomic regions. PigGIS gathers 3.84 million whole genome shotgun (WGS) records generated by the Sino–Danish Pig Genome Project, 870 084 expressed…

OryzaGenome
Dataset

OryzaGenome

Provides genome sequence/variant information for wild Oryza species together…

Provides genome sequence/variant information for wild Oryza species together with that of several cultivated strains, in close collaboration with Oryzabase, ensuring easy access to information about…

SNPchiMp
Dataset

SNPchiMp

A multi-species database to disentangle the SNP chip jungle. Features of…

A multi-species database to disentangle the SNP chip jungle. Features of SNPchiMp include, but are not limited to, the following functions: 1) referencing the SNP mapping information to the latest…

SNPfisher
Web

SNPfisher

A user-friendly web resource for manipulating and incorporating genetic…

A user-friendly web resource for manipulating and incorporating genetic variation data into your experiments. The SNPfisher website includes the SNPfisher Variant Reporter tool, which provides the…

SnapperDB
Dataset

SnapperDB

Stores bacterial variant data to facilitate reproducible and scalable analysis…

Stores bacterial variant data to facilitate reproducible and scalable analysis of bacterial populations. SnapperDB is a solution that was made to embark on whole genome sequencing pathogen…

SalmoBase
Dataset

SalmoBase

Provides an informational resource about Salmonid species. SalmoBase contains…

Provides an informational resource about Salmonid species. SalmoBase contains atlantic salmon genome reference, annotation and gene expression data. It offers a genome browser that allows users to…

tbvar
Dataset

tbvar

Provides a much needed compendium of genomic variants and their annotations for…

Provides a much needed compendium of genomic variants and their annotations for M. tuberculosis complex (MTBC) and provides the first step toward accelerating genotype–phenotype correlations in the…

RiTE-db
Dataset

RiTE-db Rice TE Database

A genus-wide collection of transposable elements and repeated sequences across…

A genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri. The database consists of more…

PlasmoView
Web

PlasmoView

Facilitates the investigation of Plasmodium falciparum (Pf) polymorphisms…

Facilitates the investigation of Plasmodium falciparum (Pf) polymorphisms across populations in malaria endemic regions and the presentation of allele frequencies on maps. The first release contains…

Pakistan whole…
Dataset

Pakistan whole genome tuberculosis

Gathers information about tuberculosis. Pakistan whole genome tuberculosis is…

Gathers information about tuberculosis. Pakistan whole genome tuberculosis is an online resource storing different types of stains about tuberculosis disease. This database was based on…

HapRice
Dataset

HapRice

A haplotype map database by using validated single nucleotide polymorphism…

A haplotype map database by using validated single nucleotide polymorphism (SNP) information for the world and Japanese rice collections. The association of SNP allele frequencies with quantitative…

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CucurbiGene
Dataset

CucurbiGene

Develops genomic tools for Squash (Cucurbita spp.) breeding: transcriptome,…

Develops genomic tools for Squash (Cucurbita spp.) breeding: transcriptome, genetic map, SNP collections and high throughput genotyping platforms applied to the competitive development of new…

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MeloGene
Dataset

MeloGene

Develops genomic tools for Melon (Cucumis melo) breeding: transcriptome, SSR,…

Develops genomic tools for Melon (Cucumis melo) breeding: transcriptome, SSR, SNP collections and high throughput genotyping platforms. Melogene includes a new version of the melon transcriptome with…

FlyVar
Dataset

FlyVar

A publicly and freely available platform that addresses the increasing need of…

A publicly and freely available platform that addresses the increasing need of next generation sequencing data analysis in the Drosophila research community. FlyVar is composed of three parts. First,…

CicArVarDB
Dataset

CicArVarDB

A repository of 1.9 million variations (SNPs and InDels) anchored on eight…

A repository of 1.9 million variations (SNPs and InDels) anchored on eight pseudomolecules in a custom database. CicArVarDB includes an easy interface for users to select variations around specific…

CerealsDB
Dataset

CerealsDB

An online resource containing a range of genomic datasets for wheat (Triticum…

An online resource containing a range of genomic datasets for wheat (Triticum aestivum) that will assist plant breeders and scientists to select the most appropriate markers for marker assisted…

Neal’s DNA…
Dataset

Neal’s DNA Mutation Site

Provides databases and softwares for analyzing mutations at the transgenic and…

Provides databases and softwares for analyzing mutations at the transgenic and bacterial lacI gene, human p53 gene and hprt gene as well as transgenic lacZ gene.

TcSNP
Dataset

TcSNP

Provides information about various strains of Trypanosoma cruzi. TcSNP gathers…

Provides information about various strains of Trypanosoma cruzi. TcSNP gathers T. cruzi sequences, multiple sequence alignments (MSAs) obtained from these sequences, single-nucleotide polymorphisms…

CGDSNPdb
Dataset

CGDSNPdb Center for Genome Dynamics Single Nucleotide Polymorphism Database

Compiles several sources of mouse single nucleotide polymorphisms (SNP) data.…

Compiles several sources of mouse single nucleotide polymorphisms (SNP) data. CGDSNPdb is composed of two different datasets: (i) the Imputed SNP Genotype Resource (IGR) which provides probable…

MGDD
Dataset

MGDD

A free web-based database that allows quick user friendly search to find…

A free web-based database that allows quick user friendly search to find different types of genomic variations among a group of fully sequenced organisms belonging to M. tuberculosis complex. The…

MTCID
Dataset

MTCID M. tuberculosis clinical isolate genetic polymorphism database

Provides a comprehensive repository to store, access and disseminate single…

Provides a comprehensive repository to store, access and disseminate single nucleotide polymorphism (SNPs) and spoligotyping profiles of M. tuberculosis. MTCID can be used to automatically upload the…

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