L519: Lab Session 11 (11/18/05)
- NCBI's dbSNP database
- Group Project Presentation
¤ dbSNP
- dbSNP comes from the National Center for Biotechnology Information (NCBI)
- SNP stands for "single nucleotide polymorphism". SNPs are the most common genetic variations and occur once every 100 to 300 bases. A key aspect of research in genetics is the association of sequence variation with heritable phenotypes. It is expected that SNPs will accelerate the identification of disease genes by allowing researchers to look for associations between a disease and specific differences (SNPs) in a population. This differs from the more typical approach of pedigree analysis which tracks transmission of a disease through a family. It is much easier to obtain DNA samples from a random set of individuals in a population than it is to obtain them from every member of a family over several generations. Once discovered, these polymorphisms can be used by additional laboratories, using the sequence information around the polymorphism and the specific experimental conditions.
- As of today, 26,430,220 records in the dbSNP
- Two types of dnSNP IDs
- rs# : Reference SNP
- ss# : Submitted SNP
- Search methods
- Simple Search : http://www.ncbi.nlm.nih.gov/SNP/
- Entrez Search : http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Snp
- Advanced Search : http://eutils.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Snp&cmd=Limits
- Data download: ftp://ftp.ncbi.nih.gov/snp/
- IUPAC Nucleotide Symbols : http://www.mun.ca/biochem/courses/3107/symbols.html
- Sequence tagged site (STS): A short (200 to 500 base pair) DNA sequence that occurs but once in the genome and whose location and base sequence are known. STSs are detectable by polymerase chain reaction (PCR), are useful for localizing and orienting the mapping and sequence data, and serve as landmarks on the physical map of a genome. Expressed sequence tags (ESTs) are STSs derived from cDNAs (complementary DNAs).
¤ Group Project Presentation
http://biokdd.informatics.indiana.edu/cgi-bin/juhur/Courses/L519FALL2005/Eval/Proj2/EvalProj2.cgi
