Genome browsers Visualization of genomic data Survey UCSC

Genome�� browsers Visualization of genomic data

Survey �� • UCSC browser • Ensembl browser • Others ?

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

Genome�� browsers Visualization of genomic data

Genome�� browsers Visualization of a gene Flat files / tab files >chr 5: 123. 004. 678 -125. 345. 112 ATGAAGTTATGGGATGTCGTGGCTGTCTGCCTGGTGCTGCTCCACACCGC GTCCGCCTTCCCGCTGCCCGCCGGTAAGAGGCCTCCCGAGGCGCCG AAGACCGCTCCCTCGGCCGCCGCCGCGCGCCCTTCGCGCTGAGCAGTGAC TGTAAGAACCGTTCCCCGCGGGGGGGCCGCCGGCGGACCCCCTCGC ACCCCCACCCGCAGCCCCGCACGTACCCCAAGCCTGATGGCT GTGTGGCCTACCGACCCGTGGGCAAGGGGTGCTGAAGCCCCCAG GGGTGCCTGGCTGCCCACTGCTGCCCGCACGCCTGAAAGTGACAC GCGCTGGTTTGCCCAGCACAGAGGGGATGGAATTTTTATGCTGCTCCTTT AGCATTCTGATGAACAAATATCCTCCCCACCAGCACCACCACCTCAGAAA Chr 5 123. 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 • 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

BLAT Blast Like Alignment Tool • BLAT (2002) • Very fast searches (My. SQL database) • Handle introns in RNA/DNA alignments • Data for more that 30 genomes (human, mouse, rat…) Splice sites Exon Intron Exon

BLAT genome Browser http: //genome. ucsc. edu//

BLAT genome Browser Using a search term or position eg Chr 1: 10, 234 -11, 567

BLAT genome Browser http: //genome. ucsc. edu/

BLAT genome Browser Using a protein or DNA sequence

Blat genome Browser

BLAT genome Browser ”Details” Correct splice site ?

Logo Plot Information Content IC = -H(p) + log 2(4) = a palog 2 pa + 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: Seq 1: A L R K P Q R T Seq 2: A V R H I L L I Seq 3: A I K V H N N T Pos 1: I = -[1*log 2(1)]+ 4. 32 = log 2(20) = 4. 32 Pos 2: I = -[1/3*log 2(1/3)+ 1/3*log 2(1/3)] + 4. 32 = 2. 73 Pos 3: I = -[2/3*log 2(2/3)+ 1/3*log 2(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

Genome�� browsers

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

SNPs

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