0
Evolutionary analysis with VAMSAS
       enabled applications:
   Sharing alignments, trees and
 annotation between intera...
FASTA




                                   GFF



               Bioinformatics
              data is not easy
         ...
Graphical Tools:
  – Visualize data and results
  – Dedicated interfaces for
    analysis methods
So, generally…
  – They ...
Graphical Tools are great…
Except when you want to go outside the box…

    devBox> funkyalign –help
      ** Funky Align ...
Visualization and Analysis of
       Molecular Sequences, Alignments and
                    Structures
                 T...
Aim: Enable user to move between
         different VAMSAS Applications


                                                ...
Positive Selection With PAML
                   http://abacus.gene.ucl.ac.uk/software/paml.html
                          ...
Workflow for Positive Selection Analysis


    Collect            How can the user
Sequence Retrieval,
                   ...
VAMSAS Data Exchange Model
                                                    Existing
• Many applications connect       ...
1. Exchange data via a Shared Document
 Accessions,
                                   VAMSAS     A
  positional          ...
2. Exchange GUI events about shared data
                                     VAMSAS     A
All shared data in
            ...
VAMSAS Tools – Now and Next
• Human DRB Analysis in Poster at ISMB (U19)
• www.vamsas.ac.uk
  – VAMSAS XML Document Schema...
Jalview 2.4
  • Released in September 2008
  • Bioinformatics App Note – January 2009
  t the BBSRC supported Jalview 2 re...
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Procter Vamsas Bosc2009

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Transcript of "Procter Vamsas Bosc2009"

  1. 1. 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
  2. 2. FASTA GFF Bioinformatics data is not easy to read….. Newick CSV PDB
  3. 3. Graphical Tools: – Visualize data and results – Dedicated interfaces for analysis methods So, generally… – They make our lives easier..
  4. 4. 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…
  5. 5. 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
  6. 6. 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
  7. 7. 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)
  8. 8. 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
  9. 9. 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
  10. 10. 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
  11. 11. 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
  12. 12. 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
  13. 13. 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...
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