Visualization of genomic data

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It og Sundhed Nov Jan. Thomas Nordahl Petersen, Associate Professor Center for Biological Sequence Analysis, DTU Normal

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Visualization of genomic data 19-Nov-18 Genome browsers Visualization of genomic data

19-Nov-18 Survey UCSC browser Ensembl browser Others ?

UCSC genome browser Basic functionalities 19-Nov-18 UCSC genome browser Basic functionalities 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 UCSC genome browser http://genome.ucsc.edu/ 19-Nov-18 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

Visualization of genomic data 19-Nov-18 Genome browsers Visualization of genomic data

Genome browsers Visualization of a gene 19-Nov-18 Genome browsers Visualization of a gene Flat files / tab files >sequence ATGAAGTTATGGGATGTCGTGGCTGTCTGCCTGGTGCTGCTCCACACCGC GTCCGCCTTCCCGCTGCCCGCCGGTAAGAGGCCTCCCGAGGCGCCCGCCG AAGACCGCTCCCTCGGCCGCCGCCGCGCGCCCTTCGCGCTGAGCAGTGAC TGTAAGAACCGTTCCCTCCCCGCGGGGGGGCCGCCGGCGGACCCCCTCGC ACCCCCACCCGCAGCCAGCCCCGCACGTACCCCAAGCCAGCCTGATGGCT GTGTGGCCTACCGACCCGTGGGCAAGGGGTGCGGGTGCTGAAGCCCCCAG GGGTGCCTGGCTGCCCACTGCTGCCCGCACGCCTGGCCTGAAAGTGACAC GCGCTGGTTTGCCCAGCACAGAGGGGATGGAATTTTTATGCTGCTCCTTT AGCATTCTGATGAACAAATATCCTCCCCACCAGCACCACCACCTCAGAAA Exon Intron Exon Chr5 123.004.678 123.404.678 124.987.012 125.345.112

Genome browsers Visualization of a gene (Ensembl) 19-Nov-18 Genome browsers Visualization of a gene (Ensembl)

Genome browsers Visualization of a gene (UCSC) 19-Nov-18 Genome browsers Visualization of a gene (UCSC) Header Exon Intron UTR

19-Nov-18 Genome browsers

19-Nov-18 Genome browsers

19-Nov-18 BLAT genome Browser http://genome.ucsc.edu//

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

19-Nov-18 BLAT genome Browser http://genome.ucsc.edu/

19-Nov-18 BLAT genome Browser Using a protein or DNA sequence

BLAT Blast Like Alignment Tool 19-Nov-18 BLAT Blast Like Alignment Tool BLAT (2002) Very fast searches (MySQL database) Handle introns in genomic alignments Data for more that 30 genomes (human, mouse, rat…) Exon Intron Exon Splice sites

19-Nov-18 Blat genome Browser

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

19-Nov-18 Splice sites

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

BLAT genome Browser ”Details” 19-Nov-18 BLAT genome Browser ”Details” Donor site | Acceptor site exon... . G | GT ...intron ...AG | exon...

19-Nov-18 Blat genome Browser

BLAT genome Browser ”Browser” 19-Nov-18 BLAT genome Browser ”Browser” Base, Center & Zoom Known genes Predictions RNA EST Expression Conservation

BLAT genome Browser Center & zoom 19-Nov-18 BLAT genome Browser Center & zoom

BLAT genome Browser Center & zoom 19-Nov-18 BLAT genome Browser Center & zoom Selected number of tracks Forward/reverse direction

BLAT genome Browser Sequence Orthologs 19-Nov-18 BLAT genome Browser Sequence Orthologs

BLAT genome Browser Sequence Orthologs 19-Nov-18 BLAT genome Browser Sequence Orthologs “klick”

BLAT genome Browser Sequence Orthologs 19-Nov-18 BLAT genome Browser Sequence Orthologs

BLAT genome Browser Sequence Orthologs 19-Nov-18 BLAT genome Browser Sequence Orthologs

BLAT genome Browser Sequence Orthologs 19-Nov-18 BLAT genome Browser Sequence Orthologs

19-Nov-18 SNPs

19-Nov-18 SNPs

19-Nov-18 Gene Sorter

19-Nov-18 Gene Sorter - homology Closest homologues

Custom tracks Upload your personal data Share data with colleagues 19-Nov-18 Custom tracks Upload your personal data Share data with colleagues Data need to be related to a reference organism

19-Nov-18 Custom tracks

19-Nov-18 Custom tracks

Exercise Basic understanding of the graphics 19-Nov-18 Exercise Basic understanding of the graphics Effect of Single Nucleotide Polymorphisms (SNPs) Finding Orthologue genes http://www.cbs.dtu.dk/courses/humanbio/2009/exercises/ExGenomeBrowser/ExGenomeBrowser.pdf