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Links tagged with 'genotype'

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Allele frequency netDatabase Content

http://www.allelefrequencies.net

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.

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

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.

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/

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

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

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

Model Organisms > Other Organisms

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

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

Genotyping - NCBITool Content

http://www.ncbi.nih.gov/projects/genotyping/formpage.cgi

Model Organisms > Other Organisms
Sequence Comparison > Other Alignment Tools

The Genotyping tool at the NCBI identifies the genotype (or subtype) of viral sequences by using a sliding window approach to BLAST analysis against reference sequences for different viral subtypes. Results are shown as a graphical output plotting the top-scoring genotype. An alignment tool is also available.

NAR Web Server Issue 2004
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tagsalgorithms dna sequence analysis genetic recombination genotype hepacivirus hepatitis b virus hiv-1 molecular sequence data sequence alignment viral dna viral genes viral genome viruses
setsNational Center for Biotechnology Information (NCBI)

HomozygosityMapperTool Content

http://www.homozygositymapper.org

DNA > Sequence Polymorphisms
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms

A web base approach to homozygosity mapping. Users upload SNP genotype files into a marker database for analysis and detection of long homozygous stretches.

NAR Web Server Issue 2009
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tagschromosome mapping genetic heterogeneity genetic linkage genotype homozygote reproducibility of results single nucleotide polymorphism

ISTECH SNPAnalyzerTool Content

http://snp.istech.info/istech/board/login_form.jsp

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.

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

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.

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/

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).

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

NCBI Influenza Virus Sequence Annotation ToolTool Content

http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/annotation.cgi

DNA > Annotations
DNA > Sequence Retrieval and Submission
Model Organisms > Other Organisms

The NCBI Influenza Virus Sequence Annotation Tool is a web application for user-provided sequences. It can predict protein sequences encoded by an input flu sequence and produce a feature table that can be used for sequence submission to GenBank.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence dna sequence analysis genotype influenza a virus influenza b virus molecular sequence data sequence alignment viral dna viral genes viral genome viruses
setsNational Center for Biotechnology Information (NCBI)

PhenomicDBDatabase Content

http://www.phenomicdb.de/

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.

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tagsanimals documentation gene expression profiling genetic databases genomics genotype humans information dissemination phenotype species specificity

PolyPhredTool Content

http://droog.gs.washington.edu/polyphred/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

UNIX-based tool for sequence trace based genotyping; integrated with Phred/Phrap/Consed (see DNA -- Contig Assembly); free for non-commercial use.

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tagsanimals antigen receptors automation base sequence dna dna sequence analysis fluorescence genotype humans molecular sequence data

PupaSuiteTool Content

http://pupasuite.bioinfo.cipf.es

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

PupaSuite is a SNP analysis tool that allows for the selection of relevant SNPs within a gene based on the characteristics of the SNP. PupaSuite also provides information about LD parameters (based on genotype data from HapMap) and identifies haplotype blocks and tag SNPs. PupaSuite was created to join PupaSNP & PupasView.

NAR Web Server Issue 2004NAR Web Server Issue 2006
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tagsalgorithms amino acid substitution binding sites genetic transcription genotype haplotypes humans linkage disequilibrium molecular evolution nucleic acid databases phenotype rna splicing single nucleotide polymorphism transcription factors

QuickSNPTool Content

http://bioinformoodics.jhmi.edu/quickSNP.pl

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.

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/

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.

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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