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ARTS -- a web-based tool for the set-up of high-throughput genome-wide mapping panels for the SNP genotyping of mouse mutants
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| Retrieve of polymorphic SNPs between multiple reference and outcross mouse strains and design SNP marker panels.
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BayGenomics -- A resource of insertional mutations in mouse embryonic stem cells
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| Search thousands of mouse embryonic stem (ES) cell lines harboring characterized insertional mutations in both known and novel genes.
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CASCAD -- a database of annotated candidate single nucleotide polymorphisms associated with expressed sequences.
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| Search for annotated information on rat and zebrafish candidate SNPs.
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CLOURE -- Clustal Output Reformatter, a program for reformatting ClustalX/ClustalW outputs for SNP analysis and molecular systematics
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| Reformat the ClustalX/ClustalW outputs to a format that is widely used in the presentation of sequence alignment data in SNP analysis and molecular systematic studies.
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Cre Transgenic Database -- Cre transgenic mouse lines with links to publications
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| Search for information Cre transgenic mouse lines. |
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DG-CST (Disease Gene Conserved Sequence Tags) -- a database of human–mouse conserved elements associated to disease genes
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| Search for sequence elements conserved between human and mouse that are involved in the pathogenesis of genetic disorders.
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DPDB -- Drosophila polymorphism database
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| Search for well-annotated polymorphic sequences in the Drosophila genus. |
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F-SNP -- computationally predicted functional SNPs for disease association studies
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| Integrates information obtained from 16 bioinformatics tools and databases about the functional effects of SNPs.
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FAMHAP -- Haplotype Association Analysis
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| An established software for haplotype association analysis of nuclear families.
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FASTSNP -- an always up-to-date and extendable service for SNP function analysis and prioritization
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| Identify and prioritize high-risk SNPs according to their phenotypic risks and putative functional effects.
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Frontiers in BioScience -- Mouse knockout database
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| Search for data regarding the phenotypes of mouse mutants rendered by the knockout of various genes.
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GenePath -- from mutations to genetic networks and back
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| Analyze mutant-based experiments and synthesize genetic networks. |
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GenoSNP -- SNP genotyping
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| A Variational Bayes within-sample SNP genotyping algorithm that does not require a reference population.
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HaploBuild -- an algorithm to construct non-contiguous associated haplotypes
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| Construct biologically relevant haplotypes that are not constrained by arbitrary length and contiguous orientation.
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Haploview -- analysis and visualization of LD and haplotype maps
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| multiplex tag SNP design
SNPs tagging
tag SNPs selection tool
tag SNPs evaluation tool
genome-wide association studies
genotyping tool
allele frequency estimation
Association mapping
disease association studies
SNPs genotyping
haplotype frequencies estimation
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Homophila -- human disease gene cognates in Drosophila
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| Study comprehensive linkage between the human disease genes compiled in Online Mendelian Inheritance in Man (OMIM) and the complete Drosophila genomic sequence.
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HuRef Genome Browser
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| A web resource for individual human genomics.
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InSNP -- a tool for automated detection and visualization of SNPs and InDels
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| Detect substitution and indel SNPs in sequencing traces.
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MITOP -- database for mitochondria-related proteins, genes and diseases
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| Search for comprehensive genetic and functional information on both nuclear- and mitochondrial-encoded mitochondrial proteins and their genes in human, mouse, yeast and other model organisms.
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MUGEN mouse database--animal models of human immunological diseases
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| Find murine models of immune processes and immunological diseases. |
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MamPol -- a database of nucleotide polymorphism in the Mammalia class
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| Conduct single nucleotide polymorphisms diversity measurements among homologous sequences from the Mammalia class.
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Mouse knockout database
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| Search the list of gene knockouts (mice) available alphabetically according to the name of the gene.
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MutDB -- interactive structural analysis of mutation data
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| Integration of publicly available databases of human genetic variation with molecular features and clinical phenotype data.
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MutaGeneSys -- estimating individual disease susceptibility based on genome-wide SNP array data
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| A system that uses genome-wide genotype data to estimate disease susceptibility.
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NRMD -- Nuclear Receptor Mutation Database
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| Search for nuclear receptor mutation information.
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ORFDB --A High-quality Open Reading Frame Collection
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| Search an evolving collection of human and mouse Open Reading Frame (ORF) clones (UltimateTM ORF Clones).
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Online Mendelian Inheritance in Animals (OMIA) -- A comparative knowledgebase of genetic disorders and other familial traits in non-laboratory animals
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| Search for up-to-date information on inherited disorders and other familial traits in non-laboratory animals.
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PADB -- published association database
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| Includes both the genetic associations and the environmental risk factors available in the PubMed database.
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PARSESNP -- a tool for the analysis of nucleotide polymorphisms
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| Display and analyze polymorphisms in genes.
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PBmice -- piggyBac Mutagenesis Information CEnter
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| A database for storing, retrieving and displaying the information derived from PB insertions (INSERTs) in the mouse genome.
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PDA -- A Pipeline to Explore and Estimate Polymorphism in Large DNA databases
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| Search for polymorphic sequences in large databases and estimate their genetic diversity.
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PDA -- Pooled DNA analyzer
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| Analyze pooled DNA.
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PIP -- a database of potential intron polymorphism markers
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| A database of potential intron polymorphism markers in plants.
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PMD -- Compilation of protein mutant data
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| Search for comprehensive information on documented protein mutants.
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PUPA SNP Finder
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| Search for single nucleotide polymorphisms (SNPs) with potential phenotypic effect.
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Pathbase -- A Database of Mutant Mouse Pathology
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| Search for images of the abnormal histology associated with spontaneous and induced mutations of both embryonic and adult mice including those produced by transgenesis, targeted mutagenesis and chemical mutagenesis.
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PolyPhred -- automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing
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| Compare fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions.
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PolymiRTS Database -- linking polymorphisms in microRNA target sites with complex traits
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| Search for naturally occurring DNA variations in putative microRNA target sites.
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Polymorphix -- a sequence polymorphism database
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| Search for information on within-species sequence polymorphism in the nuclear, mitochondrial and chloroplastic genomes of Eukaryota species. |
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PoooL -- an efficient method for estimating haplotype frequencies from large DNA pools
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| Estimate frequencies of single-nucleotide polymorphism (SNP) haplotypes from DNA pools.
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PupaSuite -- finding functional single nucleotide polymorphisms for large-scale genotyping purposes
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| Select single nucleotide polymorphisms (SNPs) with potential phenotypic effect.
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PupasView -- a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes
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| Select single nucleotide polymorphisms (SNPs) with potential phenotypic effect.
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SIFT -- predicting amino acid changes that affect protein function
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| Predict what amino acid substitutions will affect protein function.
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SNP Consortium
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| Search for Single nucleotide polymorphisms (SNPs) from the SNP Consortium (TSC), a public/private collaboration that has to date discovered and characterized nearly 1.8 million SNPs (as of 2002).
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SNP Function Portal -- a web database for exploring the function implication of SNP alleles
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| Identify the potential biological impact of genetic markers and complex relationships among genetic markers and genes using this database of SNP alleles.
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SNP-RFLPing -- restriction enzyme mining for SNPs in genomes
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| Find suitable restriction enzymes for assays on a batch of SNPs and genes from the human, rat, and mouse genomes.
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SNP-VISTA -- an interactive SNP visualization tool
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| Visualize SNPs and mutations in genes.
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SNPAnalyzer -- a web-based integrated workbench for single-nucleotide polymorphism analysis
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| Perform essential statistical analyses of SNPs in a common computational environment.
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SNPCEQer II -- the integrated detection and analysis of SNPs in DNA sequences
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| Detect and analyze single nucleotide polymorphisms (SNPs).
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SNPHunter -- a bioinformatic software for single nucleotide polymorphism data acquisition and management.
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| Search, filter, and retrieve SNP from NCBI dbSNP.
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SNPSTR -- a database of compound microsatellite-SNP markers
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| Search for information on compound microsatellite-SNP markers in human, dog, mouse, rat and chicken.
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SNPServer -- a real-time SNP discovery tool
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| Carry out real-time discovery of SNPs (single nucleotide polymorphisms) within DNA sequence data.
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SNPSplicer -- systematic analysis of SNP-dependent splicing in genotyped cDNAs
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| Conduct systematic analysis of SNP-dependent splicing in genotyped cDNAs.
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SNPdetector -- A Software Tool for Sensitive and Accurate SNP Detection
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| Perform automated identification of SNPs and mutations in fluorescence-based resequencing reads.
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SNPmasker -- automatic masking of SNPs and repeats across eukaryotic genomes
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| Carry out automatic masking of SNPs and repeats across eukaryotic genomes.
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SNPsFinder -- a web-based application for genome-wide discovery of single nucleotide polymorphisms in microbial genomes
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| Conduct genome-wide identification of SNPs in microorganisms.
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SOURCE -- A unified genomic resource of functional annotations, ontologies, and gene expression data
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| Search for information on the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus.
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Software for optimization of SNP and PCR-RFLP genotyping to discriminate many genomes with the fewest assays
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| Optimize the selection of microbial forensic markers to maximize information gained from the fewest assays, accepting whole or partial genome sequence data as input.
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StSNP -- Structure SNP
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| A web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways.
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Strainer -- a multi-platform visualization tool for metagenomics data
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| Software for analysis of population variation in community genomic datasets.
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TBASE -- a computerized database for transgenic animals and targeted mutations
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| Search for information on transgenic animals and targeted mutations generated and analyzed worldwide.
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TOM -- a web-based integrated approach for identification of candidate disease genes
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| Identify candidate disease genes using various publicly available genetic data.
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TRDB — The Tandem Repeats Database
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| Search for various information and analyze repeats in genomic DNA. |
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Tagger -- Selection and evaluation of tag SNPs
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| Select and evaluate taged SNPs from genotype data.
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The Center for Modeling Human Disease Gene Trap resource
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| Search for insertions in genes (Gene trap mutagenesis) expressed in mouse embryonic stem cells, under specific in vitro conditions, or based upon sequence identity via an online searchable database.
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The Human Chromosome Aberration Database (HCAD) -- closing the gap between breakpoints and genes
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| Search for published textual and comprehensive information on all human chromosome breakpoints.
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The Protein Mutant Database
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| Search for compiled information on artificial and natural protein mutants.
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The imprinted gene and parent-of-origin effect database now includes parental origin of de novo mutations
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| Search for information on imprinted genes and parental origin of de novo mutations.
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VNTRDB -- a bacterial variable number tandem repeat locus database
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| Search for sequence information on microbial Variable number tandem repeats.
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Variation resources at UC Santa Cruz
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| Search for comprehensive information on polymorphisms in various organisms.
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VarySysDB -- a human genetic polymorphism database based on all H-InvDB transcripts
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| A database on genetic polymorphism.
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WatCut -- An on-line tool for restriction analysis, silent mutation analysis, and SNP analysis
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| Perform oligo sequence silent mutation analysis, restriction analysis, and
scanning for amplification-created restriction sites for the detection of single nucleotide polymorphisms. |
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YH database -- the first Asian diploid genome
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| Browse and download data from the first Asian diploid genome.
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coliSNP -- clue of life SNP
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| A database server mapping nsSNPs on protein structures.
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dbGap -- a Database of Genome Wide Association Studies
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| Search for data from wide association (GWA) studies. |
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dbSNP -- EntrezSNP
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| Find the presence of Single Nucleotide Polymorphism in a nucleotide sequence.
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hapConstructor -- automatic construction and testing of haplotypes in a Monte Carlo framework
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| A tool for exploring multi-locus associations in candidate genes and regions.
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nsSNPAnalyzer -- identifying disease-associated nonsynonymous single nucleotide polymorphisms
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| Identify disease-associated nsSNPs from a large number of neutral nsSNPs.
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rSNP_Guide -- A database system for analysis of transcription factor binding to DNA with variations
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| Investigate the influence of mutations in regulatory gene regions onto DNA interaction with nuclear proteins. |
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