Transcript Tutorial_12 (2014)

Tutorial 12
Genome browser
Genome browser
• Free, open source, online browser for
genomes.
• Contains ~100 genomes, from
nematodes to human.
• Many tools that can be used to analyze
genomic data.
Genome browser
http://genome.ucsc.edu/
How to find a gene of interest?
genome
Genome
assembly
location
OR
Gene
name
Lets take a look at the gene
Information about
the gene
Sequences +Links
to other databases
Expression
data
Structural
information
RNA
secondary
structure
Basic tracks
RefSeq id
Other names
Summary
on the
gene
Genomic
position
Gene
length
Sequences
mRNA
length
Protein sequence,
mRNA sequence
Conservation
Zoom in to compare base level
Zooming in can help us identifying
alternative splicing events
Additional tracks
Literature track
RNA-Seq and regulation
Common SNPs
Tables
How to download a gene sequence?
Clade,
genome,
assembly
Group and
track
“Known genes”
table
position
Choose
“sequence”
Different parts
of the gene
Other possible tracks from the
table browser
miRNAs in the human genome
Adding custom tracks
browser position chr17:41243452-41277500
track name=unknown description="unknown genomic element" color=255,0,0,
chr17
41244000
41246000
Here’s our custom track!
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks
BLAT
BLAT
• BLAT on DNA is designed to quickly find
sequences of 95% and greater similarity of
length 25 bases or more.
• BLAT is not BLAST. DNA BLAT works by keeping
an index of the entire genome in memory. The
index consists of all overlapping 11-mers
stepping by 5.
• Protein BLAT works in a similar manner
:
:
Examples
1. In which chromosome can you find the CFTR
gene in human?
2. In which chromosome can you find the CFTR
gene in mouse?
3. How many exons does the CFTR gene have?
4. Which genes are close to CFTR on chromosome 7?
Zooming out
5. What is the orientation of the gene? Plus or minus?
6. download the promoter area of the CFTR gene (1000
bp)