VISTA v2

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VISTA

• Materials prepared by
• Steffen Schmidt, Ph.D.
• www.openhelix.com

Version_2_1007
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VISTA Agenda

• Introduction and Credits
• VISTA Browser
• VISTA Servers
• mVISTA (with rankVISTA plots)
• rVISTA
• GenomeVISTA
• Phylo-VISTA
• VISTA Enhancer Browser
• Whole-Genome rVISTA
• Summary
• Exercises

• Introduction and Credits

VISTA resource http//genome.lbl.gov/vista
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Comparative Genomics Introduction
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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
Other VISTA-related Projects

• VISTA homepage http//genome.lbl.gov/vista
• Access servers, browsers, other information

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VISTA Introduction
104637349 GTAGTGCCACTGAGTGTGACAGGGATGGCAAGAAAAGCA
TTAAGTTCCAAGGGGAAAGAA 104637408 gtgtgtgtgtgtgtgtgt

ltltltltltltltltlt 052290302
GAGATGTCACCAAGTA-AACAGAGATGGCAAGAGGACCAATAGGTTCTAG
TGGGAAAGAC 052290360
sliding window to measure sequence
conservation (default window size 100bp)
gt70 identity
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VISTA Servers
VISTA Servers
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VISTA Browser
VISTA Browser
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VISTA Overview Other Projects
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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 NHLBI/NIH US Department of Energy

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Publications

• Publications and citation information
• Access to downloads

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VISTA Agenda

• Introduction and Credits
• VISTA Browser
• VISTA Servers
• mVISTA (with rankVISTA plots)
• rVISTA
• GenomeVISTA
• Phylo-VISTA
• VISTA Enhancer Browser
• Whole-Genome rVISTA
• Summary
• Exercises

VISTA resource http//genome.lbl.gov/vista
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VISTA Browser Access
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VISTA Browser Input Menu
Java 2, if needed
base genome
position
visualization

• Choose base genome
• for comparisons
• Select location
• Determine visualization preference

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VISTA Browser Base Genome
Human May 2004

• Select a genome
• Note new versions and species added over time

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VISTA Browser Position
select

• Can be coordinates chr9104622838-104769991
• Can be a gene symbol or name
• If multiple matches, select from list

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VISTA Browser Result
Menu Icons
Position on chromosome
Control Panel
Graphical display of genome alignments (wraps
over multiple rows)
1 row
Cursor Info
Color Legend
Curve annotation (species)
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VISTA Browser Alignment Details
direction
exon
gene
repeats
SNPs
alignment
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VISTA Browser Options
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VISTA Browser Options
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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 species
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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. mouse
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 Text Browser
mouse sequence
rankVISTA
human sequence
outputs
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VISTA Browser rankVISTA Text
rankVISTA
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VISTA Browser rankVISTA Graphic
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VISTA Browser rankVISTA Graphic
rankVISTA data
rankVISTA data
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VISTA Browser Access to UCSC Browser
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VISTA Agenda

• Introduction
• VISTA Browser
• VISTA Servers
• mVISTA (with rankVISTA plots)
• rVISTA
• GenomeVISTA
• Phylo-VISTA
• VISTA Enhancer Browser
• Whole-Genome rVISTA
• Summary
• Exercises

VISTA resource http//genome.lbl.gov/vista
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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
your email
upload file
or GenBank ID

• Provide your email address
• Upload your sequences
• Or enter GenBank ID

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mVISTA Input Parameters

• AVID
• multiple pair wise alignments
• accepts finished or draft sequences

• LAGAN
• true multiple alignments

• Shuffle-LAGAN
• multiple pair wise alignments
• detects sequence rearrangements and inversions

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mVISTA Input Parameters
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mVISTA Results
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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

• Introduction
• VISTA Browser
• VISTA Servers
• mVISTA
• rVISTA
• GenomeVISTA
• Phylo-VISTA
• VISTA Enhancer Browser
• Whole-Genome rVISTA
• Summary
• Exercises

VISTA resource http//genome.lbl.gov/vista
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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
display

• Emailed results will provide a link
• Choose which binding sites matrices to display
• You can then choose visualization options

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rVISTA Results Graphic
sites
sequences

• 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

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VISTA Agenda

• Introduction
• VISTA Browser
• VISTA Servers
• mVISTA
• rVISTA
• GenomeVISTA
• Phylo-VISTA
• VISTA Enhancer Browser
• Whole-Genome rVISTA
• Summary
• Exercises

VISTA resource http//genome.lbl.gov/vista
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GenomeVISTA Access
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GenomeVISTA Input
paste sequence
or upload file
or GenBank ID
compare to
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GenomeVISTA Results
our query
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VISTA Agenda

• Introduction
• VISTA Browser
• VISTA Servers
• mVISTA
• rVISTA
• GenomeVISTA
• Phylo-VISTA
• VISTA Enhancer Browser
• Whole-Genome rVISTA
• Summary
• Exercise

VISTA resource http//genome.lbl.gov/vista
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Phylo-VISTA Access
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Phylo-VISTA Access
example
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Phylo-VISTA Example
Phylogenetic tree
Alignment Overview
Graphical display of selected region
Color legend
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VISTA Agenda

• Introduction
• VISTA Browser
• VISTA Servers
• mVISTA (with rankVISTA plots)
• rVISTA
• GenomeVISTA
• Phylo-VISTA
• VISTA Enhancer Browser
• Whole-Genome rVISTA
• Summary
• Exercise

VISTA resource http//genome.lbl.gov/vista
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VISTA Enhancer Browser Access
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VISTA Enhancer Browser Overview
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VISTA Enhancer Browser Computational Dataset
select or
search
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VISTA Enhancer Browser Computational Dataset
filters
region
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VISTA Enhancer Browser Tested Regions
negative enhancer
positive enhancer
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VISTA Enhancer Browser Experimental Data
keyword
pattern
advanced
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VISTA Agenda

• Introduction
• VISTA Browser
• VISTA Servers
• mVISTA
• rVISTA
• GenomeVISTA
• Phylo-VISTA
• VISTA Enhancer Browser
• Whole-Genome rVISTA
• Summary
• Exercise

VISTA resource http//genome.lbl.gov/vista
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Whole Genome rVISTA Access
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Whole Genome rVISTA Select Alignment
upstream range
IDs or symbols
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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

• Introduction
• VISTA Browser
• VISTA Servers
• mVISTA (with rankVISTA plots)
• rVISTA
• GenomeVISTA
• Phylo-VISTA
• VISTA Enhancer Browser
• Whole-Genome rVISTA
• Summary
• Exercises

VISTA resource http//genome.lbl.gov/vista
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VISTA Browser and rankVISTA
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

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VISTA Servers

• mVISTA create your own sequence alignments
• rVISTA and Whole Genome rVISTA identify
  conserved transcription factor binding sites
• GenomeVISTA align your sequences with genomes
• Phylo-VISTA analyze multiple DNA sequence
  alignments from different species
• wgVISTA to align sequences up to 10 Mb

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VISTA Enhancer Browser

• Enhancer Browser
• Combines computational and experimental data

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Discoveries with Medical Applications
Pennachio et al. 2001 Science 294169-73
Emison et al. 2005 Nature 434857-63

• Many scientists are using VISTA in their research

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VISTA Summary
updates
VISTA Servers (submit your own data)
VISTA Browser
Other Projects
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VISTA Agenda

• Introduction
• VISTA Browser
• VISTA Servers
• mVISTA (with rankVISTA plots)
• rVISTA
• GenomeVISTA
• Phylo-VISTA
• VISTA Enhancer Browser
• Whole-Genome rVISTA
• Summary
• Exercises

VISTA resource http//genome.lbl.gov/vista