BLAT Blast Like Alignment Tool

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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

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)]+ 4.32 = log2(20) = 4.32 Pos2: I = [1/3*log2(1/3)+ 1/3*log2(1/3)+ 1/3*log2(1/3)] + 4.32 = 2.73 Pos3: I = [2/3*log2(2/3)+ 1/3*log2(1/3) + 4.32 = 3.38

11-Apr-19 Logo Plot Exon

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

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

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)

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

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’