vistaintro slides v3(2) - lawrence berkeley national...
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Copyright OpenHelix. No use or reproduction without express written consent 1
VISTA
Materials prepared by: Warren C. Lathe III Mary E. Mangan www.openhelix.com
Version_3_1109
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VISTA Agenda
Introduction and Credits VISTA Servers
mVISTA rVISTA GenomeVISTA wgVISTA
VISTA Precomputed Alignments VISTA Browser VISTA-Point Whole Genome rVISTA
Summary Exercises
VISTA resource: http://genome.lbl.gov/vista
Introduction and Credits
Copyright OpenHelix. No use or reproduction without express written consent 4
Comparative Genomics Introduction
Human
Drosophila Mouse Urchin Chimp
Similar Genes Synteny
Sequence Alignment
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Comparative Genomics Introduction
VISTA: focus is comparative genomics
Broad range of species for comparative analysis (animals, plants, fungi, bacteria)
Full set of pre-computed comparative data
Comparative analysis of user-submitted data
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VISTA Homepage
VISTA Servers (submit your own data)
VISTA Browsers (precomputed alignments)
Other VISTA-related Projects
VISTA homepage: http://genome.lbl.gov/vista Access servers, browsers, other information
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VISTA Introduction
�sliding window� to measure sequence conservation (default window size 100bp)
Graphical presentation of sequence conservation as �peaks-and-valley� curve
>70% identity
base sequence coordinates
% identity
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wgVISTA Align and compare sequences, including microbial assemblies
mVISTA Align and compare sequences
rVISTA Search for TFBS combined with a
comparative sequence analysis
VISTA Servers
GenomeVISTA
Align DNA sequence to a genome
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VISTA Browser Browse through pre-computed
whole-genome alignments
Whole Genome rVISTA
Whole genome analysis for conserved TFBS over-represented
in upstream regions of genes
Precomputed Alignments
VISTA-Point Browse and obtain sequence and
alignment data
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SNP-VISTA!Visualization of mutations in genes
and discovery of recombination points
VISTA Overview: Other Projects
TreeQ-VISTA!Interactive tree visualization tool
Enhancer Browser!Exploration of
human enhancer activity
Phylo-VISTA!Using phylogenetic relationships to
visualize DNA similarity
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VISTA Credits
Developed & hosted at the Genomics Division of Lawrence Berkeley National Laboratory
Collaboration & Contribution UC Berkeley Stanford UC Davis
Supported by the Office of Biological and Environmental Research, US DOE.
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Publications
Publications and citation information Access to downloads
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VISTA Agenda
VISTA resource: http://genome.lbl.gov/vista
Introduction and Credits VISTA Servers
mVISTA rVISTA GenomeVISTA wgVISTA
VISTA Precomputed Alignments VISTA Browser VISTA-Point Whole Genome rVISTA
Summary Exercises
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mVISTA: Access
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mVISTA: Interface
Our example will show 3 sequences Align up to 100 sequences
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mVISTA: Input of Sequences
Provide your email address Upload your sequences Or enter GenBank ID
your email upload file
or GenBank ID
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AVID multiple pair wise alignments accepts finished or draft sequences
LAGAN true multiple alignments
mVISTA: Input Parameters
Shuffle-LAGAN multiple pair wise alignments detects sequence rearrangements and inversions
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mVISTA: Input Parameters
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mVISTA: Results
VISTA Browser VISTA-Point
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rVISTA: Access
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rVISTA: Interface
your email sequences
rVISTA sequence submission: set number Submit email address, sequences, and set parameters Key step: click the box for: Find potential transcription factors
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rVISTA: Select TRANSFAC Matrices
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rVISTA: Mailed Results
Emailed results will provide a link Choose which binding sites matrices to display You can then choose visualization options
display
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rVISTA: Results Graphic
Blue all transcription factor (TF) binding sites Red TF sites which are aligned in both sequences Green TF sites which are aligned & in conserved
regions
sequences
sites
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GenomeVISTA: Access
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GenomeVISTA: Input
paste sequence
or upload file
or GenBank ID
compare to
our query
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GenomeVISTA: Results
VISTA Track VISTA-Point VISTA Browser
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wgVISTA: Large Scale Sequence Comparison
wgVISTA: whole genome VISTA Compares 2 sequences (up to 10 Mb) Draft or finished microbial assembly sequences can be used
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VISTA Agenda
VISTA resource: http://genome.lbl.gov/vista
Introduction and Credits VISTA Servers
mVISTA rVISTA GenomeVISTA wgVISTA
VISTA Precomputed Alignments VISTA Browser VISTA-Point Whole Genome rVISTA
Summary Exercises
Copyright OpenHelix. No use or reproduction without express written consent 30
VISTA Browser: Access
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VISTA Browser: Input Menu
genome position visualization
Java 2, if needed
Choose �base� genome Select location Determine visualization preference
VISTA Browser
VISTA tracks on UCSC Browser
VISTA-Point
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VISTA Browser: Base Genome
Human May 2006
Select a genome Note: new versions and species added over time
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VISTA Browser: Position
Can be coordinates: chr9:104622838-104769991 Can be a gene symbol or name If multiple matches, select from list
select
symbol name
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VISTA Browser: Result
Position on chromosome
Control Panel
Graphical display of genome alignments
Color Legend
Cursor Info
Menu & Icons
Curve annotation (species)
1 row
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VISTA Browser: Alignment Details
direction
exon repeats
alignment
SNPs gene
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VISTA Browser: Options
Print / Save
Shift displayed region to left or right
Enlarge / Shrink alignment displayed region
Add / Remove selected alignment
Undo / Redo
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VISTA Browser: Options
Access all alignment-related information and more
Retrieve sequence alignment of displayed region
Alter display parameter
Access UCSC Genome Browser with VISTA Tracks
Get help Copyright OpenHelix. No use or reproduction without express written consent 38
VISTA Browser: Control Panel
change base
change position
change annotation
add species add/remove rows
see nucleotides
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VISTA Browser: Add Species
select different dog genome alignment Copyright OpenHelix. No use or reproduction without express written consent 40
VISTA Browser: Curve Parameter Panel
Default settings for new species curve See manual for parameter details Change later with �curve parameters� button
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VISTA Browser: Zooming
vs. rhesus
vs. dog
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VISTA Browser: Viewing Contigs
contigs contigs
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VISTA Browser: Alignment Details
click here
Click an alignment or annotation to select it Then �i� button for information
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VISTA Browser: Access to UCSC Browser
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VISTA Browser: rankVISTA Graphic
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VISTA Browser: rankVISTA Graphic
rankVISTA data rankVISTA data
click here
VISTA Point: Introduction
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VISTA Point: Access Overview
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VISTA Point: Navigation
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VISTA Point: Navigation
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VISTA Point: Graphics Table
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VISTA Point: AlignmentsTable
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sequence
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VISTA Point: Alignments Table
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align MFA
CNS rVISTA
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Whole Genome rVISTA: Access
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Whole Genome rVISTA: Select Alignment
IDs or symbols
upstream range
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Whole Genome rVISTA: Results
sites found
view genes
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Whole Genome rVISTA: Gene Results
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VISTA Agenda
VISTA resource: http://genome.lbl.gov/vista
Introduction and Credits VISTA Servers
mVISTA rVISTA GenomeVISTA wgVISTA
VISTA Precomputed Alignments VISTA Browser VISTA-Point Whole Genome rVISTA
Summary Exercises
Copyright OpenHelix. No use or reproduction without express written consent 59
VISTA Servers mVISTA: create your own sequence alignments
rVISTA: identify conserved transcription factor binding sitesg sites
GenomeVISTA: align your sequences with genomes
wgVISTA:to align sequences up to 10 Mb
Copyright OpenHelix. No use or reproduction without express written consent 60
VISTA Browser and rankVISTA
Convenient tool to display genome alignments Display of multiple alignments to find conserved
regions throughout various genomes Access to displayed alignment in various formats
rhesus
dog
horse
rankVISTA
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VISTA Point
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VISTA-related Publications
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VISTA Summary
VISTA Servers (submit your own data)
Precomputed Alignments
updates
Copyright OpenHelix. No use or reproduction without express written consent 64
VISTA Agenda
VISTA resource: http://genome.lbl.gov/vista
Introduction and Credits VISTA Servers
mVISTA rVISTA GenomeVISTA wgVISTA
VISTA Precomputed Alignments VISTA Browser VISTA-Point Whole Genome rVISTA
Summary Exercises