https://www.youtube.com/watch?v=R86d-4NXV-k /mnt/1T-5e7/mycodehtml/Biology/SangSooKim/Bioinformatics_basic/004/003_Search_data_in_dbSNP/main.html ================================================================================ - Let's search SNP named as ================================================================================ www.ncbi.nlm.nih.gov ================================================================================ ================================================================================ Click SNP ================================================================================ Click SNP ID ================================================================================ - Some people has A, some other people have G ================================================================================ - Chromosome, X, 123886270th base pair ================================================================================ ================================================================================ - XIAP is intron variant (or missense variant) which causes amino acid changes, - Nonsense variant is the case where termination codon is created? ================================================================================ ================================================================================ ================================================================================ 23th chromosome (X chromosome) 123020120th base pair "originally G" is changed to A ================================================================================ mRNA coding codon: 608th ================================================================================ - 203th location Cys is changed to Tyr ================================================================================ ================================================================================ ================================================================================ ================================================================================ - missense: case where amino acid changes ================================================================================ - nonsense: case where "termination" codon is created ================================================================================ ================================================================================ - To specific this variant, - 2 base pairs are used - left 30 bp sequence from SNP - right 30 bp sequence from SNP - By using above 2 as PCR primer, - you perform PCR on DNA - Then, some people show A, and some other people show T - which is variant SNP ================================================================================ - Unlike above example, this case has 2 50 bp sequences 50 bp R 50 bp R: variant of A or G ================================================================================ - Nucleotide symbols degenerate R: pu[r]ine group bases; A or G Y: p[y]rimidine group bases; C or T ================================================================================ ================================================================================ Easier search with specifying database (SNP)