Evolutionary analysis with VAMSAS
enabled applications:
Sharing alignments, trees and
annotation between interactive tools
Jim Procter
j.procter@dundee.ac.uk
Geoff Barton
www.vamsas.ac.uk
www.jalview.org
www.topali.org
BOSC09 Bio*Update Session 28th June 2009

FASTA
GFF
Bioinformatics
data is not easy
to read…..
Newick
CSV
PDB

Graphical Tools:
– Visualize data and results
– Dedicated interfaces for
analysis methods
So, 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
Neither efficient or usable
Usage :
funkyalign [-h|RANDOM] <Input> <Output>
OK for one-off analysis task
Where Input is a set of sequences in
funky format.
Not at all good for N methods
Where Output is a set of Funky trees,
and M parameters sets
alignments, and predicted residue functions
as Funky annotation documents.
Really
Options: bad when new tool
Parse new
is also GUI based…
-Reallygoodmodel
result format
-Align only
and import
-No holds barred…

Visualization and Analysis of
Molecular Sequences, Alignments and
Structures
TOPALi v2 AstexViewer@MSD-EBI
Evolution & Phylogeny Structure analysis
Jalview v2
Alignment, Analysis, Pierre Marguerite
Iain Milne Figure Generation
Dominik Lindner Tom Oldfield
Frank Wright
Andrew Waterhouse
David Marshall
Jim Procter
David Martin, Geoff Barton

Aim: Enable user to move between
different VAMSAS Applications
AstexViewer
TOPALi
@MSD-EBI
Why do
this ???
Jalview
Model Selection
Phylogeny
Ancestral Databases, Annotation Structure Databases
Sequences Alignment Structural Clustering
Positive Selection 2-ary Structure Prediction Uniprot/MSD Mapping
Recombination

Positive Selection With PAML
http://abacus.gene.ucl.ac.uk/software/paml.html
Amino
codon
• Infer distribution of ω over
Acid
GTC V
sites GAT
GAC
D
D
ω= dN
dS
# Non-synonymous mutation
# Synonymous Mutation
GAC
GAT
D
D
GCT A
Purifying 1 Positive GAT D
Selection ω Selection Mutations
(conservation) (specialization)
Synonymous:
– Infer Sites under positive D (0,0,1)
selection Non-Synonymous:
• estimating P(ω>1) VD (0,1,1)
AD (0,1,2)
VA (0,1,1)

Workflow for Positive Selection Analysis
Collect How can the user
Sequence Retrieval,
Align
Editing and alignment.easily move between
Sequences
applications ?
Visualize cDNA
Build Tree alignment annotation
How can the user on orthologous
save the analysis and protein structure
return to them later ?
Model Visualize
dN/dS at sites under
Phylogeny
& Positive site
eachSelection selection
Analysis

VAMSAS Data Exchange Model
Existing
• Many applications connect bioinformatics
application.
to one document.
VAMSAS
• Hide details behind API logic
Shared
• VAMSAS client library VAMSAS VAMSAS
data Client API
– Session Discovery
– Shared data access/update Private
– Session Events application
data store
• Document updates
• Others join or leave session

1. Exchange data via a Shared Document
Accessions,
VAMSAS A
positional Shared
Client P
maps and data
cross refs Library I
SEQUENCES, ALIGNMENTS
TREES AND ANNOTATION App requests
lock and updates
JAR containing document
VAMSAS XML
Document
References
JALVIEW
DATA Library provides
Provenance DATA
TOPALI others with lock
DATA
after document
is updated
Updates
input data GUI
and VAMSAS A
calculation Client P
parameters Library I

2. Exchange GUI events about shared data
VAMSAS A
All shared data in
Client P
VAMSAS
Library I
document has a
unique ID
SEQUENCES, ALIGNMENTS
TREES AND ANNOTATION
VAMSAS IDs used
in GUI Event Broadcast
References
JALVIEW
DATA
•Mouse Overs
Provenance DATA
TOPALI
DATA •Selected Regions
VAMSAS A
Client P
Library I

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
t the BBSRC supported Jalview 2 release
No• Final
Jalview to be supported until 2014 by a new
UK Biotechnology and Biological Sciences
tools and resources grant
Thank
You...