Transcript I = -[1/3*log 2 (1/3)+ 1/3*log 2 (1/3)+ 1/3*log 2 (1/3)] + 4.32 = 2.73

Genome browsers
Visualization of genomic data
survey
• How many have used a genome browser ?
• UCSC browser ?
• Ensembl browser ?
• Others ?
Genome browsers
Visualization of genomic data
Genome browsers
Visualization of a gene
Flat files / tab files
>sequence
ATGAAGTTATGGGATGTCGTGGCTGTCTGCCTGGTGCTGCTCCACACCGC
GTCCGCCTTCCCGCTGCCCGCCGGTAAGAGGCCTCCCGAGGCGCCCGCCG
AAGACCGCTCCCTCGGCCGCCGCCGCGCGCCCTTCGCGCTGAGCAGTGAC
TGTAAGAACCGTTCCCTCCCCGCGGGGGGGCCGCCGGCGGACCCCCTCGC
ACCCCCACCCGCAGCCAGCCCCGCACGTACCCCAAGCCAGCCTGATGGCT
GTGTGGCCTACCGACCCGTGGGCAAGGGGTGCGGGTGCTGAAGCCCCCAG
GGGTGCCTGGCTGCCCACTGCTGCCCGCACGCCTGGCCTGAAAGTGACAC
GCGCTGGTTTGCCCAGCACAGAGGGGATGGAATTTTTATGCTGCTCCTTT
AGCATTCTGATGAACAAATATCCTCCCCACCAGCACCACCACCTCAGAAA
Chr5
123.004.678
123.404.678 124.987.012
125.345.112
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.
Genome browsers
Visualization of a gene (Ensembl)
Genome browsers
Visualization of a gene (UCSC)
Exon
Intron
UTR
Genome browsers
Genome browsers
Genome browsers
• UCSC genome browser
• http://genome.ucsc.edu/
• Easy to use
• Often updates, but not as often as Ensembl
• upload of personal tracks
• Ensembl browser
• http://www.ensembl.org/index.html
• Less easy to use
• Maintained/updated by several people
• Gbrowser
• http://www.gmod.org/GBrowse
UCSC genome browser
Basic functionalities
• Finding a gene
• by name
• by sequence
• Gene structure
• Sequence orthologues
• Single Nucleotide Polymorphisms
• Gene Sorter - sort according to expression, homology ...
• Custom tracks
BLAT genome Browser
http://genome.ucsc.edu//
BLAT genome Browser
Using a search term or position eg Chr1:10,234-11,567
BLAT genome Browser
http://genome.ucsc.edu/
BLAT genome Browser
Using a protein or DNA sequence
BLAT
Blast Like Alignment Tool
• BLAT (2002)
• Very fast searches (MySQL database)
• Handle introns in RNA/DNA alignments
• Data for more that 30 genomes (human, mouse, rat…)
Splice sites
Exon
Intron
Exon
Blat genome Browser
BLAT genome Browser
”Details”
Correct splice site ?
Logo Plot
Information Content
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
Logo Plot
Exon
BLAT genome Browser
”Details”
Correct splice site ?
BLAT genome Browser
”Details”
Donor site |
Acceptor site
exon... . G | GT ...intron ...AG | exon...
Blat genome Browser
BLAT genome Browser
”Browser”
Known genes
Predictions
RNA
EST
Expression
Conservation
Base,
Center &
Zoom
BLAT genome Browser
Center & zoom
BLAT genome Browser
Center & zoom
Selected number of tracks
Forward/reverse direction
BLAT genome Browser
Sequence Orthologs
BLAT genome Browser
Sequence Orthologs
“klick”
BLAT genome Browser
Sequence Orthologs
BLAT genome Browser
Sequence Orthologs
BLAT genome Browser
Sequence Orthologs
SNPs
SNPs
Chromosomal locus
• A locus is a physical location on a chromosome
• p the ‘short arm’
• q the ‘long arm’
• A locus range may describe a location of a gene
• 22q11.21-q11.23
QuickTi me™ and a
decompressor
are needed to see thi s pi ctur e.
22q12.2
Chromosome
Arm
Band
Sub-band
22
q
12
2
Chromosomal locus
Searching with gene name
Chromosomal locus
Searching with locus range
Custom tracks
• Upload your personal data
• Share data with colleagues
• Data need to be related to a reference organism
Custom tracks
Custom tracks
Exercise
1.
2.
3.
4.
Basic understanding of the graphics
Effect of Single Nucleotide Polymorphisms (SNPs)
Finding Orthologue genes
Identify chromosomal locus for a gene