1. Visualization of genomic data
16-Nov-18
Genome browsers 
Visualization of genomic data

2. 16-Nov-18
16-Nov-18
Survey 
UCSC browser
Ensembl browser
Others ? 2

3. UCSC genome browser Basic functionalities used in exercise
16-Nov-18
16-Nov-18
UCSC genome browser Basic functionalities used in exercise 
Finding a gene
by name
by sequence
Gene structure
Orthologues – i.e. functional homolog in other organisms
SNP’s - Single Nucleotide Polymorphisms
Several other functionalities
Gene Sorter - sort according to expression, homology, in situ images of genes in different tissues
Custom tracks – upload your own data 3

4. Visualization of genomic data
16-Nov-18
Genome browsers 
Visualization of genomic data

5. Genome browsers Visualization of a gene
16-Nov-18
Genome browsers Visualization of a gene 
Flat files / tab files
>chr5:
ATGAAGTTATGGGATGTCGTGGCTGTCTGCCTGGTGCTGCTCCACACCGC
GTCCGCCTTCCCGCTGCCCGCCGGTAAGAGGCCTCCCGAGGCGCCCGCCG
AAGACCGCTCCCTCGGCCGCCGCCGCGCGCCCTTCGCGCTGAGCAGTGAC
TGTAAGAACCGTTCCCTCCCCGCGGGGGGGCCGCCGGCGGACCCCCTCGC
ACCCCCACCCGCAGCCAGCCCCGCACGTACCCCAAGCCAGCCTGATGGCT
GTGTGGCCTACCGACCCGTGGGCAAGGGGTGCGGGTGCTGAAGCCCCCAG
GGGTGCCTGGCTGCCCACTGCTGCCCGCACGCCTGGCCTGAAAGTGACAC
GCGCTGGTTTGCCCAGCACAGAGGGGATGGAATTTTTATGCTGCTCCTTT
AGCATTCTGATGAACAAATATCCTCCCCACCAGCACCACCACCTCAGTAA
Exon
Intron
Exon
Chr
Open Reading Frame (ORF) – from start to stop codon

6. Genome browsers Why graphic Display ?
16-Nov-18
Genome browsers Why graphic Display ? 
Why is a graphic display better than Flat files / tab files
A graphic display is compact
Meta data available i.e. Support information about a gene
Experimental evidence like EST
Predicted gene structures
SNP information
Links to many databases
In short much data about a gene is gathered is one place
and can be viewed easily.

7. Genome browsers Visualization of a gene (Ensembl)
16-Nov-18
Genome browsers Visualization of a gene (Ensembl) 

8. Genome browsers Visualization of a gene (UCSC)
16-Nov-18
Genome browsers Visualization of a gene (UCSC) 
Exon Intron UTR

9. Genome browsers  UCSC genome browser http://genome.ucsc.edu/
16-Nov-18
Genome browsers 
UCSC genome browser
Easy to use
Often updates, but not as often as Ensembl
upload of personal tracks
Ensembl browser
Less easy to use
Maintained/updated by several people
Gbrowser

10. BLAT Blast Like Alignment Tool
16-Nov-18
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

11. 16-Nov-18
BLAT genome Browser

12. 16-Nov-18
BLAT genome Browser
Using a search term or position eg Chr1:10,234-11,567

13. 16-Nov-18
BLAT genome Browser

14. 16-Nov-18
BLAT genome Browser
Using a protein or DNA sequence

15. 16-Nov-18
Blat genome Browser

16. BLAT genome Browser ”Details”
16-Nov-18
BLAT genome Browser ”Details”
Correct splice site ?

17. Logo Plot Information Content
16-Nov-18
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

18. 16-Nov-18
Logo Plot
Exon

19. BLAT genome Browser ”Details”
16-Nov-18
BLAT genome Browser ”Details”
Correct splice site ?

20. BLAT genome Browser ”Details”
16-Nov-18
BLAT genome Browser ”Details”
Donor site | Acceptor site
exon... . G | GT ...intron ...AG | exon...

21. 16-Nov-18
Blat genome Browser

22. BLAT genome Browser ”Browser”
16-Nov-18
BLAT genome Browser ”Browser”
Base,
Center &
Zoom
Known genes
Predictions
RNA
EST
Expression
Conservation

23. 16-Nov-18
Genome browsers 

24. 16-Nov-18
Genome browsers 

25. BLAT genome Browser Center & zoom
16-Nov-18
BLAT genome Browser Center & zoom

26. BLAT genome Browser Center & zoom
16-Nov-18
BLAT genome Browser Center & zoom
Selected number of tracks
Forward/reverse direction

27. BLAT genome Browser Sequence Orthologs
16-Nov-18
BLAT genome Browser Sequence Orthologs

28. BLAT genome Browser Sequence Orthologs
16-Nov-18
BLAT genome Browser Sequence Orthologs
“klick”

29. BLAT genome Browser Sequence Orthologs
16-Nov-18
BLAT genome Browser Sequence Orthologs

30. BLAT genome Browser Sequence Orthologs
16-Nov-18
BLAT genome Browser Sequence Orthologs

31. BLAT genome Browser Sequence Orthologs
16-Nov-18
BLAT genome Browser Sequence Orthologs

32. 16-Nov-18
SNPs

33. 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)

34. 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

35. 16-Nov-18
SNPs

36. 16-Nov-18
SNPs

37. Exercise Basic understanding of the graphics
16-Nov-18
Exercise
Basic understanding of the graphics
Effect of Single Nucleotide Polymorphisms (SNPs)
Finding Orthologue genes
Identify chromosomal locus for a gene