1. BLAT Blast Like Alignment Tool
11-Apr-19
BLAT Blast Like Alignment Tool
BLAT (2002)
Very fast searches (MySQL database)
Handle introns in RNA/DNA alignments
Check that donor/acceptor rules are followed
Data for more that 30 genomes (human, mouse, rat…)
Exon Intron Exon
Splice sites
Donor
site
Acceptor
site GT AG

2. Logo Plot Information Content
11-Apr-19
IC = -H(p) + log2(4)
= a palog2pa + 2
The Information content is calculated from a multiple sequence alignment.
Result is a graphical visualization of sequence conservation where:
Total height at a position is the Information Content
Height of single letter is proportional to the frequency of that letter
Mutiple alignment of 3 protein sequences:
Seq1: A L R K P Q R T
Seq2: A V R H I L L I
Seq3: A I K V H N N T
Pos1: I = [1*log2(1)] = log2(20) = 4.32
Pos2: I = [1/3*log2(1/3)+ 1/3*log2(1/3)+ 1/3*log2(1/3)] = 2.73
Pos3: I = [2/3*log2(2/3)+ 1/3*log2(1/3) = 3.38

3. 11-Apr-19
Logo Plot
Exon

4. BLAT genome Browser ”Details”
11-Apr-19
BLAT genome Browser ”Details”
Correct splice site ?

5. BLAT genome Browser ”Details”
11-Apr-19
BLAT genome Browser ”Details”
Donor site | Acceptor site
exon... . G | GT ...intron ...AG | exon...

6. Single Nucleotide Polymorphism SNP
SNPs can be located anywere in the genome
non synomous (nsSNP) i.e. amino acid is changed (shown below )
Synomous SNP does not affect the the protein
V I T P
An amino acid is coded by 3 nucleotides
Valine (V): GTC
Humans are diploid: cells have 2 homologous copies of each chromosome i.e. 2*23 chromosomes. Haploid cells only 23 chromosomes (sex-cells)

7. Diploid organism - most mammals
An example of two homologous copies of ex chromosome 9 within a cell
A chromosome from mother
A chromosome from father
If the red strand is the plus-strand: C;T (or T;C but we write it alphabetical)
If the green strand is the minus strand: G;A but we write it as G;A

8. SNP nomenclature
SNPs within a coding region of a piece of DNA might cause a change in the translated protein ie. SNPs within an exon region. Also, SNPs at the boundary of intron/exon regions can have an effect on the protein product.
nsSNP (non-synonymous SNP)
cSNP (coding SNP)
missense SNPs or mutations: nsSNP and cSNP.
nonsense SNPS are those that result in a stop-codon
SNPs within an exon region that do NOT change the protein product
sSNP (synonymous SNP)
ATG 5’