procter vamsas bosc2009
TRANSCRIPT
Geoff Barton
www.vamsas.ac.ukwww.jalview.orgwww.topali.org
BOSC09 Bio*Update Session 28th June 2009
Evolutionary analysis with VAMSAS enabled applications:
Sharing alignments, trees and annotation between interactive tools
Bioinformatics data is not easy
to read…..Newick
CSV
GFF
PDB
FASTA
Graphical Tools:– Visualize data and results– Dedicated interfaces for
analysis methodsSo, generally…
– They make our lives easier..
Graphical Tools are great… Except when you want to go outside the box…
devBox> funkyalign –help
** Funky Align version 0.0.0.b
Usage :
funkyalign [-h|RANDOM] <Input> <Output>
Where Input is a set of sequences in funky format.
Where Output is a set of Funky trees, alignments, and predicted residue functions as Funky annotation documents.
Options:
-Reallygoodmodel
-Align only
-No holds barred…
Parse new result formatand import
OK for one-off analysis task
Not at all good for N methods and M parameters sets
Really bad when new tool is also GUI based…
Neither efficient or usable
Jalview v2Alignment, Analysis,
Figure Generation
TOPALi v2
Evolution & Phylogeny
AstexViewer@MSD-EBI
Structure analysis
Visualization and Analysis of Molecular Sequences, Alignments and
Structures
Iain Milne
Dominik Lindner
Frank Wright
David Marshall
Pierre Marguerite
Tom Oldfield
Andrew Waterhouse
Jim Procter
David Martin, Geoff Barton
Jalview
TOPALi AstexViewer@MSD-EBI
Aim: Enable user to move between different VAMSAS Applications
Databases, AnnotationAlignment
2-ary Structure Prediction
Structure DatabasesStructural Clustering
Uniprot/MSD Mapping
Model SelectionPhylogenyAncestral
SequencesPositive Selection
Recombination
Why do this ???
Positive Selection With PAML
GTCGATGACGACGATGCTGAT
VDDDDAD
Mutations
Synonymous:
D (0,0,1)
Non-Synonymous:
VD (0,1,1)
AD (0,1,2)
VA (0,1,1)
ω
1Purifying
Selection(conservation)
Positive
Selection(specialization)
ω =
codonAminoAcid
http://abacus.gene.ucl.ac.uk/software/paml.html
• Infer distribution of ω over sites
dN # Non-synonymous mutationdS # Synonymous Mutation
– Infer Sites under positive selection
• estimating P(ω>1)
Align
Build Tree
Visualize sites under selection
Workflow for Positive Selection Analysis
Model dN/dS at each site
Collect Sequences
Visualize cDNAalignment annotation
on orthologousprotein structure
Phylogeny& Positive Selection
Analysis
Sequence Retrieval, Editing and alignment.
How can the user easily move between
applications ?
How can the user save the analysis and return to them later ?
VAMSAS Data Exchange Model
• Many applications connect to one document.
• Hide details behind API• VAMSAS client library
– Session Discovery– Shared data access/update– Session Events
• Document updates• Others join or leave session
Existing bioinformatics application.
VAMSAS Client API
VAMSAS logic
Private application data store
Shared VAMSAS
data
JALVIEWDATA
JALVIEWDATA
DATADATATOPALIDATA
TOPALIDATA
SEQUENCES, ALIGNMENTSTREES AND ANNOTATION
ReferencesReferences
ProvenanceProvenance
1. Exchange data via a Shared DocumentAccessions, positional maps and cross refs
input data and
calculation parameters
JAR containing VAMSAS XML
Document
VAMSASClientLibrary
A
P
I
VAMSASClientLibrary
A
P
I
App requests lock and updates
document
Library provides others with lock after document
is updatedUpdates GUI
Shared data
JALVIEWDATA
JALVIEWDATA
DATADATATOPALIDATA
TOPALIDATA
SEQUENCES, ALIGNMENTSTREES AND ANNOTATION
ReferencesReferences
ProvenanceProvenance
2. Exchange GUI events about shared data
All shared data in VAMSAS
document has a unique ID
VAMSASClientLibrary
A
P
I
VAMSASClientLibrary
A
P
I
VAMSAS IDs used in GUI Event Broadcast
•Mouse Overs•Selected Regions
VAMSAS Tools – Now and Next• Human DRB Analysis in Poster at ISMB (U19)• www.vamsas.ac.uk
– VAMSAS XML Document Schema– Java VAMSAS Client Library
• VAMSAS Publication– In the pipeline
• The VAMSAS Tools ?– TOPALi v2 App Note published
• Active development is paused– VAMSAS enabled GPL AstexViewer
• unpaid development
Jalview 2.4
• Released in September 2008• Bioinformatics App Note – January 2009• Final BBSRC supported Jalview 2 releaseNot the
Jalview to be supported until 2014 by a new UK Biotechnology and Biological Sciences tools and resources grant
Thank
You...