Genomics and Personalized Care in Health Systems
Lecture 5 Genome Browser
Leming Zhou, PhDSchool of Health and Rehabilitation Sciences
Department of Health Information Management
Genome Browser• Genome Browser is a computer program which helps to
display gene maps, browse the chromosomes, align genes or gene models with ESTs or contigs etc.
• Big Three:– UCSC Genome Browser – NCBI Mapviewer– Ensemble
UCSC Genome Browser: http://genome.ucsc.edu
NCBI Mapviewer
Ensemble
The UCSC Genome Browser
Slides adopted from OpenHelix training materials
UCSC Genome Browser• http://genome.ucsc.edu
Genome Browser Gateway• Use this Gateway to search by:
– Gene names, symbols, IDs– Chromosome number: chr7, or region: chr11:1038475-1075482– Keywords: kinase, receptor
• See lower part of page for help with format
Genome Browser Gateway
The Genome Browser Gateway
Make your Gateway choices:1. Select Clade2. Select genome = species: search 1 species at a time3. Assembly: the official backbone DNA sequence4. Position: location in the genome to examine5. Image width: how many pixels in display window; 5000 max6. Configure: make fonts bigger + other choices
4 51 32
assembly
6
The Genome Browser Gateway
• Sample search: human, March 2006 assembly, tp53
select
Select from results list ID search may go right to a viewer page, if unique
Sample Genome Viewer Image, TP53 Region
base position
UCSC genes
RefSeq genes
mRNAs & ESTs
repeats
many species compared
SNPs
single species compared
MGC clones
Visual Cues on the Genome Browser
Track colors may have meaning—for example, UCSC Gene track:• If there is a corresponding PDB entry = black• If there is a corresponding reviewed/validated seq = dark blue• If there is a non-RefSeq seq = lightest blue
Tick marks; a single location (STS, SNP)
For some tracks, the height of a bar is increased likelihood of an evolutionary relationship (conservation track)
Intron and direction of transcription <<< or >>>
<exon exon exon< < < < < < <ex 5' UTR3' UTR
Alignment indications (Conservation pairs: “chain” or “net” style)• Alignments = boxes, Gaps = lines
Options for Changing Images: Upper Section
• Change your view or location with controls at the top• Use “base” to get right down to the nucleotides• Configure: to change font, window size, more…
– Next item, next exon navigation assistance can be turned on
Specifya
position
Fonts,window,
next item,more
Walkleft orright
Zoomin
Zoomout
Click tozoom 3x
and re-center
Annotation Track Display Options
• Some data is ON or OFF by default• Menu links to info about the tracks: content, methods• You change the view with pulldown menus• After making changes, REFRESH to enforce the change
enforcechange
s
Enforcechanges
Change track view
Links to infoand/or filters
Annotation Track Options Defined• Hide: removes a track from view Dense: all items collapsed into a single line
Squish: each item = separate line, but 50% height
Pack: each item separate, but efficiently stacked (full height)
Full: each item on separate line
Mid-page Options to Change Settings
• You control the views• Use pulldown menus• Configure options page
Reset, back to defaults Start from
scratch
Enforce any changes (hide, full, squish…)
Flip display to Genomic 3’5’
Cookies and Sessions• Your browser remembers where you were (cookies)
To clear your “cart” or parameters, click default tracks or reset
OR
Save your setup as “sessions” and store/share them
Click Any Viewer Object for Details
Example: click your mouse anywhere on the TP53 line
Click the item
New description web page opens
Many details and links
to more data about TP53
Get DNA, with Extended Case/Color Options• Use the DNA link at
the top• Plain or Extended
options• Change colors, fonts,
etc.
Base Level and Protein Sequences
BLASTX Search to Confirm the Protein
Get Sequence from Details Pages
Click a track, go to Sequence section of details page
Click the item
sequence sectionon detail page
Accessing the BLAT Tool
• BLAT = BLAST-like Alignment Tool– Rapid searches by INDEXING the entire genome– Works best with high similarity matches
BLAT• BLAT on DNA is designed to quickly find sequences of 95% and
greater similarity of length 25 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 25 bases, and sometimes find them down to 20 bases.
• BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more.
• In practice DNA BLAT works well on primates, and protein BLAT on land vertebrates
• BLAT works by keeping an index of the entire genome in memory. The index consists of all non-overlapping 11-mers except for those heavily involved in repeats.
• http://genome.ucsc.edu
BLAT Search
Make choices
DNA limit 25000 basesProtein limit 10000 aa
25 total sequences
Paste one or more sequences
Or upload
submit
BLAT Results with Hyperlinks
• Results with demo sequences, settings default; sort = Query, Score– Score is a count of matches—higher number, better match
• Click browser to go to Genome Browser image location (next slide)• Click details to see the alignment to genomic sequence (2nd slide)
sorting
go to
bro
wse
r/vie
wer
go to
alig
nmen
t det
ail
BLAT Results: Browser
• From browser click in BLAT results• A new line with Your Sequence from BLAT Search appears! Base position = “full” menu and zoomed in enough to see amino acids
in 3 frame translation
query
BLAT Results,Alignment Details
Your query
Genomic match, color cues
Side by Side Alignment
yoursgenomic
Summary
• UCSC Genome Browser• Visual cues and genomic context• Many ways to alter your views• Access to deeper data• Access and use sequence data
UCSC Table Browser
The Table Browser
Open browser
Open browser
Table Browser
34
Many Other Databases Use UCSC Genome Browser Mirror and Software
• Malaria: http://areslab.ucsc.edu/• Arabidopsis: http://epigenomics.mcdb.ucla.edu/• Archaea: http://archaea.ucsc.edu/• GSID HIV Browser: http://www.gsid.org/• GEP Drosophila Genome Browser: http://gander.wustl.edu• …
GEP Drosophila Genome Browser• UCSC Genome Browser, GEP version, parts of genomes, GEP
data, used for annotation of Drosophila species
– http://gander.wustl.edu
Male Drosophila melanogasterhttp://en.wikipedia.org/wiki/Drosophila_melanogaster
Drosophila melanogaster Chromosomes
http://en.wikipedia.org/wiki/Drosophila_melanogaster
Fruit Flies and Human Disease Research• About 75% of known human disease genes have a
recognizable match in the genetic code of fruit flies, and 50% of fly protein sequences have mammalian analogues.
• An online database called Homophila is available to search for human disease gene homologues in flies and vice versa.
• Drosophila is being used as a genetic model for several human diseases including the neurodegenerative disorders Parkinson's, Huntington's, spinocerebellar ataxia and Alzheimer's disease.
• The fly is also being used to study mechanisms underlying aging and oxidative stress, immunity, diabetes, and cancer, as well as drug abuse.
Homework 4• Read through the BLAST tutorial (IntroToBLAST.zip, A simple Introduction
to NCBI BLAST) and follow the instructions to reproduce the results described in the tutorial. List the steps you have taken and indicate whether you find any differences from the results mentioned in the tutorial.
• Use the sequence of BRCA1 gene, run a BLAT search against human genome (the most recent assembly, GRCh37), select the best sequence alignment result and view the output in the genome browser. You should provide a screen shot of the obtained page, which should include at least the gene, its homolog genes, other refseq, mRNA, the gene in other species, SNPs, and repeats. – Obtain mRNA-Genomic Alignments record from the browser– Obtain the predicted protein sequence from the browser– Obtain the precise location of one SNP record in the genome sequence– Zoom in to the base level and determine the protein sequence corresponding to
one well conserved exon; get the DNA sequence of the exon, run a blastx search (do not apply low complexity filtering) to confirm the correctness of the protein sequence you obtain