UCSC GenomeBrowser
Dror Hollander
Gil Ast Lab
Sackler Medical School
Understanding the Genome
DNA
RNA
protein
miRNA
gene expression
non-coding RNA
secondary structure
alternative splicing
exon-intron structure
histonemidifications
genes
GC content
promoters
repetitive elements
conservation
SNPs
nucleosomeoccupancy
How can you examine a genomic segment while
taking all of these factors into account?
Lecture Overview
UCSC Genome Browser
Interface & selected tracks
Detecting alternative splicing events
Chromatin organization & epigenetics
BLAT
PCR
Galaxy
UCSC Genome Browser
Basic design: “the Genome Browserstacks annotation tracks beneathgenome coordinate positions,allowing rapid visual correlation ofdifferent types of information”
genome
track
track
(64 eukaryote
genomes)
Genome Browsing…
Basic Genome Browser Interface
UTR
CDS
intron
genedirection
(> / <)
chromosomalposition
genomiccoordinates
zoom
RefseqGenestrack
UCSCGenestrack
mark and drag hereto zoom in
•Black - feature has a corresponding entry in the Protein Data Bank (PDB)
•Dark blue - transcript has been reviewed or validated by either the RefSeq, SwissProt or CCDS staff
•Medium blue - other RefSeq transcripts
•Light blue - non-RefSeq transcripts
start codons ingreen
stop codons inred
Basic Genome Browser Interface
Configure track visualization:
Basic Genome Browser Interface
“RefSeq track shows known human protein-coding andnon-protein-coding genes taken from the NCBI RNAreference sequences collection (RefSeq). The data areupdated daily”
“The UCSC track shows gene predictions based on datafrom RefSeq, Genbank, CCDS and UniProt… includes bothprotein-coding and putative non-coding transcripts…Compared to RefSeq, this gene set has generally about10% more protein-coding genes, approximately five timesas many putative non-coding genes, and about twice asmany splice variants”
Let’s examine a few examples online…
Basic Genome Browser Interface
A few more tracks worth mentioning:
miRNA (Genes and Gene Prediction Tracks ->sno/miRNA)
conservation (Comparative Genomics ->Conservation)
Expression tracks
Regulation tracks (chromatin structure andmodifications, DNA methylation, etc.; includesENCODE data)
RNA secondary structure (Genes and GenePrediction Tracks -> EvoFold)
SNPs (Variation and Repeats -> SNPs)
Basic Genome Browser Interface
Convert browser window to animage file:
Get genomic DNA for the viewedcoordinates:
Convert sequence to a differentgenome assembly or genome:
Lecture Overview
UCSC Genome Browser
Interface & selected tracks
Detecting alternative splicing events
Chromatin organization & epigenetics
BLAT
PCR
Galaxy
Detecting Alternative Splicing Events
Via Human mRNAs & Spliced ESTstracks (mRNA and EST Tracks)
gene DNA
mRNA
“The mRNA track shows alignments betweenhuman mRNAs in GenBank and the genome”
“…alignments between human expressedsequence tags (ESTs) in GenBank and thegenome… ESTs are single-read sequences,typically about 500 bases in length”
Detecting Alternative Splicing Events
Via Alt Events track (Genes and GenePrediction Tracks) – based on UCSC genes
gene DNA
>
cassetteExon
Detecting Alternative Splicing Events
Via Burge RNA-seq track (Expression)
Click on the track name to choosetissues
gene DNA
Burge
RNA-seq
Different Alternative Splicing Types
Lecture Overview
UCSC Genome Browser
Interface & selected tracks
Detecting alternative splicing events
Chromatin organization & epigenetics
BLAT
PCR
Galaxy
Histone Modifications
Transcription Factor Binding
DNA Methylation
Lecture Overview
UCSC Genome Browser
Interface & selected tracks
Detecting alternative splicing events
Chromatin organization & epigenetics
BLAT
PCR
Galaxy
BLAT
BLAT = Blast-Like Alignment Tool
BLAT is designed to find similarity of>95% on DNA and >80% forprotein
BLATquery
BLATquery
Lecture Overview
UCSC Genome Browser
Interface & selected tracks
Detecting alternative splicing events
Chromatin organization & epigenetics
BLAT
PCR
Galaxy
PCR
temperatures
ampliconin fastaformat
coordinates
strand
primers
amplicon
Lecture Overview
UCSC Genome Browser
Interface & selected tracks
Detecting alternative splicing events
Chromatin organization & epigenetics
BLAT
PCR
Galaxy
Galaxy
“Galaxy allows you to do analysesyou cannot do anywhere elsewithout the need to install ordownload anything. You cananalyze multiple alignments,compare genomic annotations,profile metagenomic samples andmuch much more...”
Galaxy – What Is It Good for?
Getting the best out of UCSC
Operating on UCSC data
Supports operations both at theinterval level, and at the sequencelevel
Designed for biologists!
Galaxy – Typical Workflow
Extract sets of coordinates
either upload from computer or fromUCSC table browser
Operate on different sets ofcoordinates (intersect, subtractetc.)
Fetch genomic sequences ofcoordinates