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Links tagged with 'genotype'

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Allele frequency netDatabase Content

http://www.allelefrequencies.net [open in a new window]

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Human Genome > Databases

The allele frequency net database is an online repository that contains information on the frequencies of immune genes and their corresponding alleles in different populations. At present, the system contains data on the frequency of genes from different polymorphic regions such as human leukocyte antigens, killer-cell immunoglobulin-like receptors, major histocompatibility complex Class I chain-related genes and a number of cytokine gene polymorphisms.

links directory index: 58
TitlePublication YearGoogle Scholar Citation Count
Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations201158
NAR Database Issue 2011
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tagscytokines gene frequency genotype haplotypes histocompatibility antigens class i humans kir receptors major histocompatibility complex nucleic acid databases

ARTSDatabase Content

http://andromeda.gsf.de/arts [open in a new window]

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DNA > Sequence Polymorphisms
Model Organisms > Mouse and Rat

ARTS (Advanced Retrieval Tool for SNPs) can be used to retrieve SNP that are polymorphic between several different mouse strains to aid in the design of genome-wide SNP marker panels.

links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
ARTS: a web-based tool for the set-up of high-throughput genome-wide mapping panels for the SNP genotyping of mouse mutants200510
NAR Web Server Issue 2005
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tagsanimals chromosome mapping genetic markers genomics genotype inbred c3h mice mice mutant strains mice single nucleotide polymorphism

FluGenomeTool Content

http://www.flugenome.org/ [open in a new window]

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Human Genome > Health and Disease
Model Organisms > Other Organisms
Sequence Comparison > Similarity Searching and Classification

FluGenome is a tool for determining lineages and genotypes of influenza A viruses.

links directory index: 41
TitlePublication YearGoogle Scholar Citation Count
FluGenome: a web tool for genotyping influenza A virus200741
NAR Web Server Issue 2007
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tagscomputational biology genetic databases genetic polymorphism genomics genotype influenza a virus orthomyxoviridae phylogeny viral genes viral genome viral proteins

Geno2phenoTool Content

http://www.geno2pheno.org/cgi-bin/geno2pheno.pl [open in a new window]

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Model Organisms > Other Organisms

Geno2pheno takes as input an HIV-1 pol-gene DNA sequence and estimates phenotypic drug resistance to 17 antiretroviral drugs.

links directory index: 363
TitlePublication YearGoogle Scholar Citation Count
Methods for optimizing antiviral combination therapies200342
Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes2003147
Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype2002174
NAR Web Server Issue 2003
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tagsalgorithms anti-hiv agents artificial intelligence automated pattern recognition cluster analysis computational biology computer-assisted drug therapy computing methodologies decision trees disease susceptibility dna sequence analysis drug combinations factual databases gene expression profiling genetic models genetic polymorphism genetic variation genotype hiv hiv infections hiv-1 humans innate immunity molecular sequence data phenotype pol genes regression analysis reproducibility of results sensitivity and specificity statistical models viral dna viral drug resistance viral genome

ISTECH SNPAnalyzerTool Content

http://snp.istech.info/istech/board/login_form.jsp [open in a new window]

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DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

ISTECH SNPAnalyzer is a tool for the statistical analysis of SNP data that includes Hardy Weinberg equilibrium (HWE), haplotype estimation, linkage disequilibrium (LD), and QTL analyses. Registration required; some browser requirements and set-up necessary.

links directory index: 38
TitlePublication YearGoogle Scholar Citation Count
SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis200538
NAR Web Server Issue 2005
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tagsalgorithms dna sequence analysis gene frequency genetic predisposition to disease genotype haplotypes humans linkage disequilibrium phenotype quantitative trait loci single nucleotide polymorphism systems integration

MIRU-VNTRplusTool Content

http://www.miru-vntrplus.org [open in a new window]

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DNA > Phylogeny Reconstruction
Human Genome > Health and Disease
Model Organisms > Microbes

MIRU-VNTRplus allows users to analyze genotyping data of their Mycobacterium tuberculosis strains either alone or in comparison with the reference DB of strains. The web server also includes tools to search for similar strains, phylogenetic analysis and mapping of geographic information.

links directory index: 116
TitlePublication YearGoogle Scholar Citation Count
MIRU-VNTRplus: a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria201018
Evaluation and strategy for use of MIRU-VNTRplus, a multifunctional database for online analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates200898
NAR Web Server Issue 2010
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tagsbacterial dna bacterial typing techniques cluster analysis dna fingerprinting genetic databases genetic polymorphism genotype humans interspersed repetitive sequences microbial sensitivity tests minisatellite repeats molecular epidemiology mycobacterium tuberculosis phylogeny restriction fragment length polymorphism tuberculosis

Mouse Genome Database (MGD)Database Content

http://www.informatics.jax.org/ [open in a new window]

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Model Organisms > Databases

The Mouse Genome Database (MGD) is the community model organism database for the laboratory mouse and the source for phenotype and functional annotations of mouse genes. MGD includes a complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information. MGD contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Major improvements to the Mouse Genome Database include comprehensive update of genetic maps, implementation of new classification terms for genome features, development of a recombinase (cre) portal and inclusion of all alleles generated by the International Knockout Mouse Consortium (IKMC).

links directory index: 318
TitlePublication YearGoogle Scholar Citation Count
The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse20125
The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics201177
The Mouse Genome Database: enhancements and updates201038
MGD: the Mouse Genome Database2003198
NAR Database Issue 2010NAR Database Issue 2011
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tagsalgorithms alleles animal models animals chromosome mapping computational biology genetic databases genetic models genome genomics genotype integrases knockout mice mice mutant strains mice nucleic acid databases phenotype terminology as topic

PhenomicDBDatabase Content

http://www.phenomicdb.de/ [open in a new window]

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Model Organisms > General Resources
Protein > Annotation and Function
Sequence Comparison > Comparative Genomics

PhenomicDB integrates the genotype and phenotype information of several organisms from public data sources. The mapping of phenotypic data fields allows cross-species phenotype comparison.

links directory index: 41
TitlePublication YearGoogle Scholar Citation Count
PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics200541
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external linksLink on Wikipedia
tagsanimals documentation gene expression profiling genetic databases genomics genotype humans information dissemination phenotype species specificity

PhenomicDBDatabase Content

http://www.phenomicdb.de [open in a new window]

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Model Organisms > Databases
Model Organisms > General Resources

PhenomicDB a free multi-organism phenotype-genotype database unifying a variety of primary sources to make phenotypic data from a wide range of species and model organisms simultaneously searchable, visible and comparable. Gene orthology and similarity information mapped to particular entries, and the phenotypic data clustering system, provide facilities for the discovery of new phenotypic manifestations of a given genotype. Reported relationships are supported by evidence and reference links.

This content is being maintained by Ivanka_Karageorgieva_metalife.

links directory index: 74
TitlePublication YearGoogle Scholar Citation Count
Phenoclustering: online mining of cross-species phenotypes20104
PhenomicDB: a new cross-species genotype/phenotype resource200729
PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics200541
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tagsanimals cluster analysis data mining documentation gene expression profiling genetic databases genomics genotype humans information dissemination phenotype rna interference species specificity

QuickSNPTool Content

http://bioinformoodics.jhmi.edu/quickSNP.pl [open in a new window]

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DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

QuickSNP is a resource for the selection of tagSNPs in the human genome that includes a gene-centric selection module.

links directory index: 13
TitlePublication YearGoogle Scholar Citation Count
QuickSNP: an automated web server for selection of tagSNPs200713
NAR Web Server Issue 2007
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tagsalgorithms animals automation chromosome mapping computational biology dna sequence analysis genetic databases genetic models genotype human genome humans linkage disequilibrium single nucleotide polymorphism

Rat Genome Database (RGD)Database Content

http://rgd.mcw.edu/ [open in a new window]

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Model Organisms > Mouse and Rat

The Rat Genome Database (RGD) is a repository of rat genetic and genomic data. As well as integrating this data with mapping, physiological and strain information, RGD also provides researchers with several tools that facilitate searching, data mining and data analysis.

links directory index: 261
TitlePublication YearGoogle Scholar Citation Count
The Rat Genome Database 2009: variation, ontologies and pathways200927
The Rat Genome Database, update 2007--easing the path from disease to data and back again2007106
The Rat Genome Database (RGD): developments towards a phenome database200545
Rat Genome Database (RGD): mapping disease onto the genome200283
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tagsanimal disease models animals cardiovascular diseases chromosome mapping database management systems disease genetic databases genetic markers genetic variation genome genomics genotype heritable quantitative trait humans inborn genetic diseases inbred strains rats mice microsatellite repeats nervous system diseases nucleic acid databases phenotype quantitative trait loci radiation hybrid mapping rats sequence homology signal transduction systems integration terminology as topic

SNP CutterTool Content

http://bioinfo.bsd.uchicago.edu/SNP_cutter.htm [open in a new window]

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DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

SNP Cutter is a tool that automates PCR-RFLP assay design for SNP genotyping.

links directory index: 37
TitlePublication YearGoogle Scholar Citation Count
SNP Cutter: a comprehensive tool for SNP PCR-RFLP assay design200537
NAR Web Server Issue 2005
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tagsdna primers dna restriction enzymes genotype humans polymerase chain reaction restriction fragment length polymorphism single nucleotide polymorphism

Virus Genotyping ToolsTool Content

http://bioafrica.mrc.ac.za/rega-genotype/html/ [open in a new window]

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DNA > Phylogeny Reconstruction
Model Organisms > Microbes

This web server facilitates high-throughput virus genotyping by aligning query sequences to a pre-defined set of reference strains and then computing phylogenetic analysis.

links directory index: 16
TitlePublication YearGoogle Scholar Citation Count
A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences200916
NAR Web Server Issue 2009
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tagsbase sequence genetic recombination genetic variation genotype hepacivirus hepatitis b virus hiv-1 phylogeny reference standards sequence alignment sequence analysis viruses

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