User:Jarle Pahr/dbSNP

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Notes on the dbSNP database:

dbSNP Classic view: http://www.ncbi.nlm.nih.gov/projects/SNP/

dbSNP Entrez:http://www.ncbi.nlm.nih.gov/snp

FTP: ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/

Question: dbSNP : best way to obtain data on SNPs: http://www.biostars.org/p/1332/


OpenHelix dbSNP tutorial: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=39

http://pga.gs.washington.edu/presentations/db_interface_tutorial.pdf

http://www.niehs.nih.gov/news/assets/docs_f_o/interactive_tutorial_i_database_interfaces_all_.pdf


https://cgsmd.isi.edu/dbsnpq/doc.php


NCBI Handbook Chapter 5 - The Single Nucleotide Polymorphism Database (dbSNP) of Nucleotide Sequence Variation: http://www.ncbi.nlm.nih.gov/books/NBK21088/


http://massgenomics.org/2012/01/the-current-state-of-dbsnp.html


http://www.snpator.org/HelpManual/loaddbsnpinfo.htm


http://blog.openhelix.eu/?tag=dbsnp&paged=2


http://seqanswers.com/forums/archive/index.php/t-13865.html

http://www.ncbi.nlm.nih.gov/books/NBK44455/

http://rbaltman.wordpress.com/tag/dbsnp/


dbSNP fact sheet: ftp://ftp.ncbi.nih.gov/pub/factsheets/Factsheet_SNP.pdf

BLAST SNP: http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_SPEC=SNP&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=dbSNP_homepage

Concepts/terminology

Access

http://www.ncbi.nlm.nih.gov/projects/SNP/batchquery.html

https://cgsmd.isi.edu/dbsnpq/

http://www.biostars.org/p/5636/

http://seqanswers.com/forums/archive/index.php/t-15863.html

http://osdir.com/ml/python.bio.general/2006-03/msg00019.html

http://hongqinlab.blogspot.no/2013/02/how-to-obtain-ncbi-dbsnp-genotype-data.html

http://osdir.com/ml/python.bio.general/2006-03/msg00022.html

http://www.biostars.org/p/64897/

http://www.bioconductor.org/packages/2.12/data/annotation/

Bibliography

dbSNP: the NCBI database of genetic variation: http://nar.oxfordjournals.org/content/29/1/308.full

Single nucleotide differences (SNDs) in the dbSNP database may lead to errors in genotyping and haplotyping studies.: http://www.ncbi.nlm.nih.gov/pubmed/19877174

New tools and methods for direct programmatic access to the dbSNP relational database: http://nar.oxfordjournals.org/content/39/suppl_1/D901.full

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