> Tag > Links tagged with 'single nucleotide polymorphism'

Links tagged with 'single nucleotide polymorphism'

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Found 43 links

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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

SNP@DomainTool Content

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

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DNA > Sequence Polymorphisms
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Domains and Motifs

SNP@Domain identifies SNPs within human protein domains allowing users to investigate SNPs in the context of two dimensional and three dimensional maps. Links to external databases (Pfam, SCOP, Ensembl, dbSNP, OMIM, SIFT) are also presented.

links directory index: 17
TitlePublication YearGoogle Scholar Citation Count
SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences200617
NAR Web Server Issue 2006
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tagshumans protein databases protein sequence analysis single nucleotide polymorphism tertiary protein structure

SNPboxTool Content

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

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DNA > Sequence Polymorphisms
DNA > Tools For the Bench
Human Genome > Sequence Polymorphisms

Tool for large-scale standardized primer design with specific modules for SNP and exon PCR amplification. Results are presented as HTML with genomic position, primer sequence, and PCR conditions. Precomputed SNPbox results for all Ensembl exons are also available on the server.

links directory index: 15
TitlePublication YearGoogle Scholar Citation Count
SNPbox: web-based high-throughput primer design from gene to genome200415
NAR Web Server Issue 2004
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tagsdna primers exons genome nucleic acid databases polymerase chain reaction single nucleotide polymorphism

SNPinfoTool Content

http://www.niehs.nih.gov/snpinfo [open in a new window]

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DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Splicing
Protein > 3-D Structure Prediction
RNA > Functional RNAs

A suite of web=based tools for SNP detection. Functional predictions of SNP affect on protein structure, gene regulation, splicing and miRNA binding are incorporated.

links directory index: 60
TitlePublication YearGoogle Scholar Citation Count
SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies200960
NAR Web Server Issue 2009
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tagsbinding sites genes genetic linkage genetic predisposition to disease genome genome-wide association study humans male micrornas prostatic neoplasms reproducibility of results rna splice sites single nucleotide polymorphism systems integration transcription factors

SNPsynTool Content

http://snpsyn.biolab.si [open in a new window]

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Expression > Gene Set Analysis
Expression > Networks
Human Genome > Sequence Polymorphisms

SNPsyn is a tool for the discovery of synergistic pairs of SNPs from large genome-wide case-control association studies data on complex diseases. The SNPsyn web server receives GWAS data submissions, invokes the interaction analysis and returns results. The user can explore details on identified SNP-SNP pairs, perform gene set enrichment analysis and interact with the constructed SNP synergy network.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
SNPsyn: detection and exploration of SNP-SNP interactions20111
NAR Web Server Issue 2011
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tagschromosome mapping genome-wide association study single nucleotide polymorphism

SVMHCTool Content

http://www-abi.informatik.uni-tuebingen.de/Services/SVMHC/ [open in a new window]

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DNA > Sequence Polymorphisms
Human Genome > Other Resources
Human Genome > Sequence Polymorphisms
Protein > Networks & Interactions, Pathways and Enzymes

SVMHC is a server for prediction of MHC class I and class II binding peptides. SVMHC can be used to find likely binders in a protein sequence and to investigate the effects of single nucleotide polymorphisms on MHC-peptide binding.

links directory index: 242
TitlePublication YearGoogle Scholar Citation Count
SVMHC: a server for prediction of MHC-binding peptides200640
Prediction of MHC class I binding peptides, using SVMHC2002202
NAR Web Server Issue 2006
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tagsalleles animals artificial intelligence computational biology histocompatibility antigens histocompatibility antigens class i hla antigens humans mice peptides predictive value of tests protein binding protein databases protein sequence analysis sensitivity and specificity single nucleotide polymorphism t-lymphocyte epitopes

TACTTool Content

http://jbirc.jbic.or.jp/tact/ [open in a new window]

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DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Human Genome > Annotations
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching and Classification

Transcriptome Auto-annotation Conducting Tool (TACT) is an automated tool for conducting functional annotation of transcripts that integrates sequence similarity searches and functional motif predictions. TACT was originally developed as an automatic annotation pipeline for the Human Full-length cDNA Annotation Invitational (H-Inv) project.

links directory index: 307
TitlePublication YearGoogle Scholar Citation Count
TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB20064
Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB)200516
Integrative annotation of 21,037 human genes validated by full-length cDNA clones2004287
NAR Web Server Issue 2006
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tagsalternative splicing amino acid motifs amino acid sequence base sequence complementary dna computational biology dna sequence analysis expressed sequence tags genes genetic databases genetic models genetic polymorphism genetic transcription human genome humans messenger rna microsatellite repeats molecular sequence data nucleic acid databases open reading frames protein databases proteins rna sequence analysis sequence analysis single nucleotide polymorphism systems integration tertiary protein structure

VARIDTool Content

http://compbio.cs.utoronto.ca/varid/ [open in a new window]

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DNA > Sequence Polymorphisms

VARiD is a Hidden Markov Model for SNP and indel identification with AB-SOLiD color-space as well as regular letter-space reads. VARiD combines both types of data in a single framework which allows for accurate predictions.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
VARiD: a variation detection framework for color-space and letter-space platforms20102
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tagsalgorithms base sequence dna sequence analysis molecular sequence data single nucleotide polymorphism
setsUniversity of Toronto

VarioWatchTool Content

http://genepipe.ncgm.sinica.edu.tw/variowatch/main.do [open in a new window]

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

VarioWatch (formerly GenoWatch) is a disease gene mining browser for association study. VarioWatch annotates both known SNPs and novel variants using information from public domain websites such as NCBI, UniProt, KEGG and GO.

links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
GenoWatch: a disease gene mining browser for association study200810
NAR Web Server Issue 2008NAR Web Server Issue 2012
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tagschromosome mapping genes genetic databases genetic markers genetic polymorphism human genome humans inborn genetic diseases internet microsatellite repeats pubmed single nucleotide polymorphism software user-computer interface

VarScanTool Content

http://varscan.sourceforge.net/ [open in a new window]

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DNA > DNA and Genomic Analysis
DNA > Sequence Polymorphisms

VarScan is a platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequency. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples.

links directory index: 94
TitlePublication YearGoogle Scholar Citation Count
VarScan: variant detection in massively parallel sequencing of individual and pooled samples200994
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tagscomputational biology dna sequence analysis humans single nucleotide polymorphism

VnDDatabase Content

http://vnd.kobic.re.kr:8080/VnD/ [open in a new window]

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Other Molecules > Databases

The variations and drugs (VnD) is a consolidated database containing information on diseases, related genes and genetic variations, protein structures and drug information. The VnD database is a useful platform for researchers studying the underlying mechanism for association among genetic variations, diseases and drugs.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
VnD: a structure-centric database of disease-related SNPs and drugs20115
NAR Database Issue 2011
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tagsdisease genetic databases humans mutation pharmaceutical preparations protein conformation proteins single nucleotide polymorphism

WhETSTool Content

http://www.rothamsted.ac.uk/whets/ [open in a new window]

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DNA > Sequence Polymorphisms
DNA > Sequence Retrieval and Submission
Model Organisms > Plants
Sequence Comparison > Similarity Searching and Classification

WhETS (Wheat Estimated Transcript Server) is a resource that combines Triticeae ESTs/mRNAs with rice genes to find the best estimate of hexaploid wheat transcript sequences for a target gene, supplemented with information on tissue distribution and likely gene structure, to aid in primer design.

This content is being maintained by RowanMitchell.

links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
Wheat Estimated Transcript Server (WhETS): a tool to provide best estimate of hexaploid wheat transcript sequence200710
NAR Web Server Issue 2007
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tagscomputational biology expressed sequence tags genetic databases genetic models plant chromosomes plant genes plant genome ploidies sequence alignment single nucleotide polymorphism triticum

WormBaseDatabase Content

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

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Model Organisms > Worm

Repository of mapping, sequencing and phenotypic information about C. elegans and C. briggsae.

links directory index: 206
TitlePublication YearGoogle Scholar Citation Count
WormBase: a comprehensive resource for nematode research201099
WormBase: a cross-species database for comparative genomics2003107
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external linksLink on Twitter Link on Wikipedia
tagsalleles animals base sequence caenorhabditis caenorhabditis elegans computational biology data collection expressed sequence tags gene expression genetic databases genomics helminth dna helminth genes helminth rna high-throughput nucleotide sequencing information storage and retrieval intergenic dna internet molecular sequence annotation neurons nucleic acid databases nucleic acid sequence homology open reading frames phenotype protein databases quality control rna interference single nucleotide polymorphism software tertiary protein structure transcription factors

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