Sequence Polymorphisms

Links to various sequence polymorphism databases and resources concerning SNPs, short deletion, insertion polymorphisms and other unique genomic features.

Found 63 links

Displaying 15 links

AutoSNPdbTool Content

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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.

links directory index: 41
TitlePublication YearGoogle Scholar Citation Count
SNPServer: a real-time SNP discovery tool200541

Cancer Genome Anatomy ProjectTool Content

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Goal is to determine the gene expression profiles of normal, precancer, and cancer cells; resources for human and mouse include ESTs, gene expression patterns, SNPs, cluster assemblies, cytogenetic information, and tools to query and analyze the data.

CARGOTool Content

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CARGO (Cancer And Related Genes Online) is a portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human.

CNVerTool Content

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CNVer is a method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. CNVer combines this information within a unified computational framework called the donor graph, allowing it to better mitigate the sequencing biases that cause uneven local coverage.

links directory index: 23
TitlePublication YearGoogle Scholar Citation Count
Detecting copy number variation with mated short reads201023

dbSNPDatabase Content

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

links directory index: 43
TitlePublication YearGoogle Scholar Citation Count
Genome-wide evaluation of the public SNP databases200343

DNA Methylation DatabaseDatabase Content

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The database contains information about the occurrence of methylated cytosines in the DNA.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count

EpiToolKitTool Content

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A suite of tools for immunological research. EpiToolKit offers a variety of prediction methods that may be run simultaneously for predicting MHC Class I and II ligands, and minor histocompatibility antigens. The influence of sequence polymorphisms or mutations on potential T-cell epitopes may also be examined.

FastSNPTool Content

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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.

GeSBAPTool Content

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Gene Set based Analysis of Polymorphisms (GeSBAP) implements the gene set analysis to the evaluation of genome wide association studies. Gene set analysis is based on testing the association of modules of functionally related genes.

GVSTool Content

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Genome Variation Server (GVS) is a database that provides access to human genotype data found in dbSNP, and tools for the analysis of genotype data.

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GWAS3DTool Content

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GWAS3D web server computes the probability of genetics variants affecting regulatory pathways and underlying disease/trait associations by integrating chromatin state, functional genomics, sequence motif, and conservation information when given GWAS data or variant list. GWAS3D also provides comprehensive annotations and visualizations to help users interpreting the results.

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HGVbaseDatabase Content

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Human Genome Variation database - curated; attempt to summarize all known sequence variations in the human genome, to facilitate research into how genotypes affect common diseases, drug responses, and other complex phenotypes.

HomozygosityMapperTool Content

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A web base approach to homozygosity mapping. Users upload SNP genotype or sequencing files for analysis and detection of long homozygous stretches between affected individuals. Human, rodent and other mammals are mappable.

This content is being maintained by dominik.

Human Genome Variation NomenclatureResource Content

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The Human Genome Society has established a committee to suggest standards for the description of sequence variants in DNA, RNA, and protein sequences. The standards are linked here.

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