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MIRU-VNTRplus / Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeat plus
Allows a robust-lineage identification based on the combination of different genotyping data. MIRU-VNTRplus is a system with a focus on evaluation of a reference database. It offers three main functions: (i) phylogenetic lineage identification by using a reference database; (ii) analysis and visualization of genotyping data; and (iii) access to the MLVA MtbC15-9 nomenclature service. It includes features minimum spanning tree (MST), geographic mapping and the nomenclature service.
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 genomic position, alternate allele read frequency, strain specificity, restriction enzyme recognition site changes and flanking primers for all SNPs and Indels in a user-defined gene or region of the zebrafish genome. The SNPfisher site also contains links to display our SNP data in the UCSC genome browser. The SNPfisher tools will facilitate the use of SNP variation in zebrafish research as well as vertebrate genome evolution.
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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 interest through BLAST sequence comparison, keyword searches of annotations derived from UniRef90 and GenBank comparisons, GO annotations or in genes corresponding to syntenic regions of reference genomes. In addition, SNPs between specific varieties may be identified for targeted mapping and association studies.
SoyKB / Soybean Knowledge Base
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, metabolites, single nucleotide polymorphisms, plant introduction lines and traits. It also incorporates many multi-omics datasets including transcriptomics, proteomics, metabolomics and molecular breeding data, such as quantitative trait loci, traits and germplasm information. Soybean Knowledge Base has a new suite of tools such as In Silico Breeding Program for soybean breeding, which includes a graphical chromosome visualizer for ease of navigation. It integrates quantitative trait loci, traits and germplasm information along with genomic variation data, such as single nucleotide polymorphisms, insertions, deletions and genome-wide association studies data, from multiple soybean cultivars and Glycine soja.
IMSR / International Mouse Strain Resource
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. IMSR is a dynamic data system that provides, for each strain or cell line, links for ordering, links to the repositories’ strain description, and links to phenotype and disease model data. The database aims to assist investigators in finding the mouse resources needed for their studies.
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, expression and mutational information about gene-breaking transposon (GBT) lines from the International Zebrafish Protein Trap Consortium (IZPTC) that includes researchers from around the globe. This resource is open to community-wide contributions including expression and functional annotation.
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 estimates of both one dimensional and multi-dimensional measures of nucleotide diversity in polymorphic sets. The website integrates the information from the databases and offers several interfaces for browsing the contents of database in different ways as well as a set of common analysis tools. It facilitates comprehensive meta-analyses involving both multi-locus and multi-species polymorphic data.
ChickVD / Chicken Variation Database
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 genes, we mapped each variant onto the RJF reference genome sequence in the context of gene annotations and other relevant features, such as genetic markers and QTLs. Therefore the ChickVD database, provides both a powerful information resource and an analysis workbench for applications in biological research, medicine and agriculture. A graphical MapView shows variants mapped onto the chicken genome in the context of gene annotations and other features, including genetic markers, trait loci, cDNAs, chicken orthologs of human disease genes and raw sequence traces. ChickVD also stores information on quantitative trait loci using data from collaborating institutions and public resources. Our data can be queried by search engine and homology-based BLAST searches.
DoGSD / Dog Genome SNP Database
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 for the study of dog's population, evolution, phenotype and life habit. DoGSD integrates some closely related information including SNP annotation, summary lists of SNPs located in genes, synonymous and non-synonymous SNPs, sampling location and breed information.
CeNDR / C. elegans Natural Diversity Resource
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, genome-wide sequence and variant data for every strain, and a GWA mapping portal for studying natural variation in Caenorhabditis elegans. CeNDR offers reduced redundancy of data collection (e.g. whole-genome sequencing) along with consistent data collection and organization as a centralized resource. The unification of strain management facilitates studies of natural variation across the wide Caenorhabditis community and beyond.
RVD / Rice Variation Database
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 omics data. IC4R was designed for scalability and sustainability, integrating data from remote resources through APIs. IC4R bears the potential to serve as a one-stop knowledgebase to make big data accessible to the rice research community and function as a valuable resource not only for plant researchers in molecular biological studies but also for breeders in rice production and improvement.
DPDB / Drosophila Polymorphism DataBase
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 greatly facilitate both multi-locus and multi-species diversity studies in one of the most important groups of model organisms. DPDB includes analysis tools for sequence comparison and the estimation of genetic diversity, a page with real-time statistics of the database contents, a help section and a collection of selected links.
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 genome assembly, 2) extraction of information contained in dbSNP for SNPs present in all commercially available bovine chips, and 3) identification of SNPs in common between two or more bovine chips (e.g. for SNP imputation from lower to higher density). This platform allows easy integration and standardization, and it is aimed at both industry and research. It also enables users to easily link the information available from the array producer with data in public databases, without the need of additional bioinformatics tools or pipelines.
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 geographical origins, phenotypic traits, mutants and genetic resources. The current version of OryzaGenome consists of genomic variants from 446 O. rufipogon accessions derived by an imputation method and variants from 17 accessions by imputation-free deeper (up to approximately 90×) sequencing along with the Os-Nipponbare-Reference-IRGSP-1.0 reference genome of O. sativa ssp. japonica cv. Nipponbare. Our goal is to establish a pan-Oryza genomic repository that covers both reference genome sequences and genomic variant information.
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 trait loci (QTLs) and functionally characterized genes could be clarified by using two other databases, Q-TARO and OGRO, constructed on the same platform. The allele frequency of each SNP can be visualized in the SNP genome browser similar to the human HapMap database. To obtain information on SNPs in any genomic region and to design cleaved amplified polymorphic sequence (CAPS) markers, we also constructed a tool for SNP searches and design of primer pairs. We also provide information for a core set of 768 SNPs selected for the analysis of genetic diversity and QTL mapping in the world rice collection.
RiTE-db / Rice TE Database
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 than 170,000 entries divided into three main types: (i) a classified and curated set of publicly-available repeated sequences, (ii) a set of consensus assemblies of highly-repetitive sequences obtained from genome sequencing surveys of 12 species; and (iii) a set of full-length TEs, identified and extracted from 12 whole genome assemblies.
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 selection. CerealsDB includes a database which currently contains in excess of 100,000 putative varietal SNPs, of which several thousand have been experimentally validated. In addition, CerealsDB contains databases for DArT markers and EST sequences, and links to a draft genome sequence for the wheat variety Chinese Spring.
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 conditions from next-generation sequencing (NGS)-generated whole-genome shotgun (WGS) datasets in Sequence Read Archive (SRA). This online resource describes homozygous single-nucleotide polymorphisms (SNPs), homozygous insertion or deletion (InDel) polymorphisms and known-gene annotations for these polymorphisms in rice, maize, and sorghum.
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 closely related pathogens. tbvar provides a user-friendly interface, closely integrated and interlinked with other major resources in the field. The tool also provides interface for annotation of known variants and identification of novel variants obtained from genome sequencing data sets and could potentially lead to application in clinical settings.
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, a database that contains 5.94 million DNA polymorphisms found in Drosophila melanogaster derived from whole genome shotgun sequencing of 612 genomes of D. melanogaster. In addition, a list of 1,094 dispensable genes has been identified. Second, a graphical user interface (GUI) has been implemented to allow easy and flexible queries of the database. Third, a set of interactive online tools enables filtering and annotation of genomic sequences obtained from individual D. melanogaster strains to identify candidate mutations. FlyVar permits the analysis of next generation sequencing data without the need of extensive computational training or resources.
Provides information about various strains of Trypanosoma cruzi. TcSNP gathers T. cruzi sequences, multiple sequence alignments (MSAs) obtained from these sequences, single-nucleotide polymorphisms (SNPs) and small indels identified derived from scanning. The database offers text-based searches for sequences based on attributes derived from their annotation. The result provides a list of genes matching the specified criteria, containing links to the corresponding MSAs, where users can visualize polymorphic sites in different colors, typefaces and styles.
Rice SNP-Seek Database
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 region, find different alleles from predefined varieties and query basic passport and morphological phenotypic information about sequenced rice lines. Users can visualize SNPs with the gene structure using JBrowse. Phylogenetic trees or multidimensional scaling plots can be used to explore evolutionary relationships between rice varieties.
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 searches are based on data generated by pair wise comparison using a tool that has already been described. Different types of variations that can be searched are SNPs, indels, tandem repeats and divergent regions. The searches can be designed to find specific variations either in a given gene or any given location of the query genome with respect to any other genome currently available.
CGDSNPdb / Center for Genome Dynamics Single Nucleotide Polymorphism Database
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 genotype and associated confidence levels for about 8 million SNPs in 74 strains of mice and (ii) data collected from over 140 strains of laboratory mice. Searches can be made by chromosome region, nearby gene annotations or SNP identifiers among about 9 686 537 distinct SNPs.
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