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Links tagged with 'single nucleotide polymorphism'

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Found 58 links

Displaying 15 links

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

AutoSNPdbTool Content

http://autosnpdb.qfab.org.au/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

SNPServer combines BLAST, cap3 and a SNP discovery module into a single pipeline for the discovery of SNPs in user submitted files or dynamically created assemblies.

NAR Web Server Issue 2005
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tagsdna sequence analysis sequence alignment single nucleotide polymorphism time factors

CADgeneDatabase Content

http://www.bioguo.org/CADgene/

DNA > Databases

The CADgene, a comprehensive manually curated database for coronary artery disease genes. Candidate genes are classified into 12 functional categories based on their roles in CAD. Each gene includes detailed information from related studies (e.g. the size of case-control, population, SNP, odds ratio, P-value, etc.) and useful annotations, which include general gene information, Gene Ontology annotations, KEGG pathways, protein-protein interactions and others.

NAR Database Issue 2011
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tagscoronary artery disease genetic databases genetic predisposition to disease humans single nucleotide polymorphism

CanPredictTool Content

http://www.cgl.ucsf.edu/Research/genentech/canpredict/

Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > Sequence Features

CanPredict uses a combination of computational methods to predict whether specific sequence changes in a protein are likely to be cancer-associated mutations.

NAR Web Server Issue 2007
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tagsalgorithms alleles amino acids computational biology expressed sequence tags genetic predisposition to disease humans missense mutation neoplasm dna neoplasms single nucleotide polymorphism tumor cell line

CaSNPDatabase Content

http://cistrome.dfci.harvard.edu/CaSNP/

Expression > Databases

CaSNP database for storing and interrogating quantitative copy number alterations (CNA) data from SNP arrays on 34 different cancer types in 104 studies. With a user input of region or gene of interest, CaSNP will return the CNA information summarizing the frequencies of gain/loss and averaged copy number for each study, and provide links to download the data or visualize it in UCSC Genome Browser. CaSNP also displays the heatmap showing copy numbers estimated at each SNP marker around the query region across all studies for a more comprehensive visualization.

NAR Database Issue 2011
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tagsdna copy number variations human genome humans neoplasms nucleic acid databases oligonucleotide array sequence analysis single nucleotide polymorphism

CASTpTool Content

http://sts.bioengr.uic.edu/castp/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing

Computed Atlas of Surface Topography of proteins (CASTp) locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins.

NAR Web Server Issue 2003NAR Web Server Issue 2006
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tagsalgorithms amino acids bacterial proteins bacteriorhodopsins binding sites enzymes ligands macromolecular substances mathematical computing molecular models myoglobin nucleic acid conformation protein conformation protein databases protein sequence analysis proteins ribonucleases sequence alignment single nucleotide polymorphism tertiary protein structure

dbDNVDatabase Content

http://goods.ibms.sinica.edu.tw/DNVs/

DNA > Databases

The duplicated gene nucleotide variants database (dbDNV) (http://goods.ibms.sinica.edu.tw/DNVs/) promotes accurate variation annotation. Aside from the flat file download, users can explore the gene-related duplications and the associated DNVs by DGL and DNV searches, respectively. In addition, the dbDNV contains 304,110 DNV-coupled SNPs. From DNV-coupled SNP search, users observe which SNP records are also variants among duplicates.

This content is being maintained by wenlin.

NAR Database Issue 2011
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tagsduplicate genes genetic variation human genome humans molecular sequence annotation nucleic acid databases single nucleotide polymorphism

dbSNPDatabase Content

http://www.ncbi.nlm.nih.gov/SNP/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

Repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms; NCBI collaboration with NHGRI.

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tagsgenetic databases human genome humans single nucleotide polymorphism
setsNational Center for Biotechnology Information (NCBI)

dbSNP-QDatabase Content

http://cgsmd.isi.edu/dbsnpq

DNA > Databases

dbSNP-Q is a web application for working with the dbSNP relational database. dbSNP is a source of information on single nucleotide polymorphisms (SNPs) and other genetic variation for many different organisms, including humans. dbSNP-Q can be used to query human data from dbSNP for a variety tasks such as genomic mapping, SNP/gene functional properties, allele frequency data and information on the underlying experiments. It also includes documentation and download tools.

This content is being maintained by ssaccone.

NAR Database Issue 2011
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tagshumans nucleic acid databases single nucleotide polymorphism

DNannotatorTool Content

http://bioapp.psych.uic.edu/DNannotator.htm

DNA > Annotations
Human Genome > Annotations

DNannotator is a tool that performs de novo annotation of SNPs, STSs, and exons. It also allows for the migration of user-defined annotations onto different versions of genomic sequences (<30Kb size limit).

This content is being maintained by cliu.

NAR Web Server Issue 2003
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tagsalgorithms dna primers dna sequence analysis gene frequency genetic databases genetic markers genomics human chromosomes human genome humans sequence alignment sequence tagged sites single nucleotide polymorphism

EnsemblDatabase Content

http://www.ensembl.org

DNA > Databases
Model Organisms > Databases

The Ensembl project provides high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish.

NAR Database Issue 2010NAR Database Issue 2011
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tagsanimals anopheles gambiae classification computational biology genetic databases genetic variation genome genomics humans mice molecular sequence annotation nucleic acid databases nucleic acid regulatory sequences open reading frames protein databases rats search engine single nucleotide polymorphism species specificity tertiary protein structure zebrafish

Ensembl GenomesDatabase Content

http://www.ensemblgenomes.org

Model Organisms > Databases

Ensembl Genomes is a new portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualisation platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualised in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site.

NAR Database Issue 2010
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tagsanimals anopheles gambiae bacterial genome classification computational biology fungal genome gene expression genetic databases genetic polymorphism genome humans invertebrates nucleic acid databases open reading frames plant genome search engine single nucleotide polymorphism tertiary protein structure

FastSNPTool Content

http://fastsnp.ibms.sinica.edu.tw

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

Function Analysis and Selection Tool for Single Nucleotide Polymorphisms (FastSNP) allows users to identify and prioritize SNPs that are likely to have functional effects.

This content is being maintained by fastsnp.

NAR Web Server Issue 2006
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tagsgene frequency genetic predisposition to disease phenotype proteins risk single nucleotide polymorphism

FoldXTool Content

http://foldx.embl.de/

Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

FOLD-X is a program for calculating the folding energies of proteins and for calculating the effect of a point mutation on the stability of a protein.

NAR Web Server Issue 2005
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tagsmolecular structure mutation nucleic acid conformation protein conformation protein databases protein folding proteins single nucleotide polymorphism

GenoWatchTool Content

http://genepipe.ngc.sinica.edu.tw/genowatch

Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms

A disease gene mining browser for association study. GenoWatch is a real-time batch SNP and short tandem repeat polymorphism pipeline that extracts current information from public domain websites such as NCBI, UniProt, KEGG and GO so that users can select the appropriate disease candidate genes.

NAR Web Server Issue 2008
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tagschromosome mapping genes genetic databases genetic markers genetic polymorphism human genome humans inborn genetic diseases microsatellite repeats pubmed single nucleotide polymorphism