Introduction to Bioinformatics - COIN81
COIN 81 Week Eight
This week we'll study SNPs and Haplotypes . Make sure to read David Cox's original paper on haplotypes, followed by his larger whole genome study. This is a rapidly growing field, and there is a significant amount of research going on.
SNPs - SNPs are an essential part of genomics, and are a recent introduction to the NCBI database. There is an exercise around SNPs that is part of the bioinformatics workshop I teach at UC Davis.
Haplotypes - Haplotypes are a natural outgrowth of the discovery of SNPs, and area a fascinating topic. Haplotypes are also discussed in an exercise which is also part of the bioinformatics workshop I teach at UC Davis.
Genotyping - genotyping is an extension of both SNPs and Haplotypes and is the last part of the SNP/Haplotype exercise. These exercises are very important, and will help you understand the nuances of human variation.
dbSNP - dbSNP is the key database within NCBI, and while it is difficult to search.
HapMap.org - HapMap project is an attempt to sequence the genomes of 10,000 diverse humans.
Perlegen - Perlegen Sciences is the engine behind the original haplotype work published by David Cox in 2001 and 2004 and other research.
SNPs exercise in the UC Davis Workshop. An introduction to searching the SNP database, and SNP genotyping.
Haplotype exercise in the UC Davis Workshop. An introduction to haplotypes and the SNP/Haplotype tools available from Perlegen Sciences.