ucsc genome browser dror hollander gil ast lab sackler medical school
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UCSC Genome Browser
Dror HollanderGil Ast Lab
Sackler Medical School
Understanding the Genome
DNARNA
protein
miRNA
gene expression
non-coding RNA
secondary structure
alternative splicing
exon-intron structure
histone midifications
genes
GC content
promoters
repetitive elements
conservation
SNPs
nucleosome occupancy
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 Browser
stacks annotation tracks beneath
genome coordinate positions,
allowing rapid visual correlation of
different types of information”
genome
track
track
(64 eukaryote
genomes)
Genome Browsing…
Basic Genome Browser Interface
UTRCDSintrongene
direction(> / <)
chromosomal position
genomic coordinates
zoom
Refseq Genes track
UCSC Genes track
mark and drag here to 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 in green
stop codons in red
Basic Genome Browser Interface
Configure track visualization:
Basic Genome Browser Interface
“RefSeq track shows known human protein-coding and
non-protein-coding genes taken from the NCBI RNA
reference sequences collection (RefSeq). The data are
updated daily”
“The UCSC track shows gene predictions based on data
from RefSeq, Genbank, CCDS and UniProt… includes both
protein-coding and putative non-coding transcripts…
Compared to RefSeq, this gene set has generally about
10% more protein-coding genes, approximately five times
as many putative non-coding genes, and about twice as
many 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 and
modifications, DNA methylation, etc.; includes ENCODE data)
RNA secondary structure (Genes and Gene Prediction Tracks -> EvoFold)
SNPs (Variation and Repeats -> SNPs)
Basic Genome Browser Interface
Convert browser window to an image file:
Get genomic DNA for the viewed coordinates:
Convert sequence to a different genome 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 ESTs tracks (mRNA and EST Tracks)
gene DNA
mRNA
“The mRNA track shows alignments between human mRNAs in GenBank and the genome”
“…alignments between human expressed sequence tags (ESTs) in GenBank and the genome… ESTs are single-read sequences, typically about 500 bases in length”
Detecting Alternative Splicing Events
Via Alt Events track (Genes and Gene Prediction Tracks) – based on UCSC genes
gene DNA
>cassetteExon
Detecting Alternative Splicing Events
Via Burge RNA-seq track (Expression)
Click on the track name to choose tissues
gene DNA
Burge RNA-seq
Different Alternative Splicing Types
Exon skipping
Alternative splice site (3’)
Intron retention
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% for protein
BLAT query
BLAT query
Lecture Overview UCSC Genome Browser
Interface & selected tracks
Detecting alternative splicing events
Chromatin organization & epigenetics
BLAT
PCR
Galaxy
PCR
temperatures
amplicon in fasta format
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 analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples and much much more...”
Galaxy – What Is It Good for?
Getting the best out of UCSC
Operating on UCSC data
Supports operations both at the interval level, and at the sequence level
Designed for biologists!
Galaxy – Typical Workflow
Extract sets of coordinates
either upload from computer or from UCSC table browser
Operate on different sets of coordinates (intersect, subtract etc.)
Fetch genomic sequences of
coordinates
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