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From Variome_net

openfree Variome.net: difference among individuals & populations in one species.

 

Point Variation

 

The variome.net is an openfree web resource and encyclopedia of world wide SNP (Single Nucleotide Polymorphism), SV, Indels, CNV, and other variants researchers. The variome.net aims to support the international genome variance researches by collecting, organizing, analyzing, and disseminating variome information.

 
What are Variome and Variomics?: 

Are humans a single species?: Yes, but with many diverse sub puplations from ancient and modern propagation.

 

Ethnic variomes:

   KoVariome  |  Chinese variome  |  Japanese variome

 

openfree variome information guildeline

 Current Research (Please list your projects here)
 

• Applications

 Service Opened!

• SNP@Web       : SNP database and tool catalogs  http://variome.kobic.re.kr/SNPatWEB/
• SNP@Domain : A web resource of Single Nucleotide Polymorphisms (SNPs) within protein domain structures and sequences
• SNP@Ethnos  :  A database of Ethnically Variant SNPs http://variome.kobic.re.kr/SNPatETHNIC/
• SNP@Promoter : A web resource of Single Nucleotide Polymorphisms (SNPs) within promoter. http://variome.kobic.re.kr/SNPatPromoter
• SNP2NMD        :  A database of human SNPs resulting NMD PTC.  http://variome.kobic.re.kr/SNP2NMD
• SNP2SPLICE (Updating!): A database of Single Nucleotide Polymorphisms within splicing sites.
• FESD                 : A web-based integrated database for selecting sets of SNPs in putative functional elements in human gene http://variome.kobic.re.kr/FESD
• ssSNPTarget (HOT!): Genome-Wide Splice-Site Single Nucleotide Polymorphism Database.  http://sssnptarget.org, http://variome.kobic.re.kr/ssSNPTarget
• MitoVariome (HOT!): A variome database of human mitochondrial DNA  http://variome.kobic.re.kr/MitoVariome
• Alternatome (Coming soon!) :  A database of alternative splicing with splicing array to understand gene regulation.
   

Under development!

• ALU2NMD        :  A database of human ALUs resulting NMD.
• Disease2Gene2SNP project with istech members
• SNP@Structural Domain : A web resource of Single Nucleotide Polymorphisms (SNPs) within structural protien domains
• Alternative Splicing Resource : A web resource for the alternative splicing events

 

• Research

• [SUBMITTED] 
  SAPs (Single Amino acid Polymorphisms) with High Levels of Population Differentiation are Enriched in Transmembrane Protein Domains
  Dataset
•  anlaysis SNPs within structural domains
•  variation of gene expression and seuqences
•  analysis SNPs within human - chimpanzee ortholog genes

 

Infra Resources

      from (KOBIC). 

      SNPpipe: a collection of automatic downloading and parsing modules  Website

Web Resources 

 

• [PUBLISHED] in Human Mutation
  ssSNPTarget : Genome-Wide Splice-Site Single Nucleotide Polymorphism Database
   

• [PUBLISHED] in BMC Bioinformatics
  MitoVariome : A variome database of human mitochondrial DNA 
   

• [PUBLISHED] in BMC Bioinformatics
  SNP@Promoter  : Human SNP databases for transcription regulatory regions.
  
   
• [PUBLISHED]
  SNP2NMD  http://variome.kobic.re.kr/SNP2NMD/ 
  : A database of human SNPs causing NMD (nonsense-mediated mRNA decay). http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/3/397
  
   
• [PUBLISHED]
  SNP@Ethnos  http://variome.kobic.re.kr/SNPatETHNIC/ 
  : A database of Ethnically Variant SNPs.
  http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D711

 

• [PUBLISHED]
  SNP@Domain  http://variome.kobic.re.kr/SnpNavigator/ or http://snpnavigator.net/
  : A web resource of Single Nucleotide Polymorphisms (SNPs) within protein domain structures and sequences.
  http://nar.oxfordjournals.org/cgi/content/full/34/suppl_2/W642   
  
   
• [PUBLISHED]
  D2SNP  http://bioportal.kobic.re.kr:8080/D2GSNP/index.faces 
  : A web-based tools for the selection of a set of SNPs within candidate genes of human diseases.
  http://www.kogo.or.kr/bulletin/UploadFile/rapidcom_1_200603.pdf

  
   

• [PUBLISHED]
  FESD http://variome.kobic.re.kr/FESD
  : A web-based integrated database for selecting sets of SNPs in putative functional elements in human gene.
  http://nar.oxfordjournals.org/cgi/content/full/33/suppl_1/D518

     
Research results

      from (KOBIC). 
 

• [PUBLISHED]
  Comparative study of the linkage disequilibrium of an ENCODE region, chromosome 7p15, in Korean, Japanese, and Han Chinese samples.
   http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=16376517

Broadly External Links

a PASNP site: Pan Asia SNP project related site.
Biopedia, 
siphs:a life sciences community,
Medicine and molecular biology DB
dbGap: a Database of Genome Wide Association Studies
FESTA tagSNP picker
Haplo, Haplot
Allele Frequency Database at Yale. USA

Q & A

Opinions 

Meetings and conferences
International Meetings on Variome
 

SNP Basics

• SNPs: Variations on a Theme - A basic introduction to SNPs from the National Center for Biotechnology Information (NCBI).
• Understanding SNPs and Cancer - An online tutorial from the National Cancer Institute.
• Diseases and Medical Response - An animated tutorial describing how DNA markers are used in medical applications. Part of the Kids Genetics Web site from GlaxoSmithKline.
• Genome Variations - Questions and answers about genome variation from the Genome News Network.
• The Cutting Edge: SNPs and Their Medical Application - From The Wellcome Trust.
• A Brief Guide to SNPs - A set of questions and answers from The Wellcome Trust.
   

Variome Server at PGI


 

Members (everyone is welcome to participate in)

• Areum Han
   
• Sung Sam Gong
• Yubok Cho
• Hyo Jin Khang
• Jong Bhak: Jong is a bioinformatist living in Asia now.
• Sohyun Hwang
• Woo-Yeon Kim
• Jin Ok Yang

Variomics and SNP References
 

    1. Prichard et al, 2000, Inference of Population Structure Using Multilocus Genotype Data, Genetics, 155, 945-959.
    2. Bowcock et al, 1994, High resolution of human evolutionary trees with polymorphic microsatellites, Nature, 368, 31, 455-457.
    3. Shriver et al, 2004, The genome distribution of population substructure in four populations using 8,524 autosomal SNPs.
    4. Shriver et al, 2005, Large-scale SNP analysis reveals clustered and continuous patterns o f human genetic variation.
    5. Adeyemo et al, 2005, Genetic structure in four West African population groups.
    6. Chakraborty and Jin, 1993, A unified approach to study hypervariable polymorphisms: Statistical considerations of determining relatedness and population distances.
 

 

 

 

 

 

 

 

• The SNP Consortium website: past, present, and future - From Nucleic Acids Research 31(1), 124-27 (2003).
• Introduction to SNPs: Discovery of Markers for Disease - From BioTechniques, June 2002 (pdf).
• Prospecting for Gold in Genome Gulch - From The Scientist, April 2002.
• Single nucleotide polymorphisms: From the evolutionary past... - From Nature, February 2001.
• Single nucleotide polymorphisms: . . .to a future of genetic medicine - From Nature, February 2001.

   

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