Protein and RNA alignment and analysis with Jalview 2.8.2 and JABA 2.1
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Transcript of Protein and RNA alignment and analysis with Jalview 2.8.2 and JABA 2.1
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Protein and RNAalignment and analysis
with Jalview 2.8.2 and JABA 2.1
TT18 and Poster B38Jim Procter
[email protected] Coordinator, Barton Group
College of Life Sciences, University of Dundee, UK.
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Standalone or web based
Java
alignmentviewerand
editor&
annotation, tree, and structure
Available at www.jalview.or
g
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One alignment, many views
Sequence features highlight key regions like functional sites
Alignment annotation area shows graphs and symbols from
calculations and manual curation
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Linked tree viewer allows subgroups to
be identified in alignment
Group selections
Colours and mouseovers
Linked Jmol viewer shows one or more
structures coloured by alignment views
Linked PCA viewer shows selections and
sequence groups
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Newick & New Hampshire Extended
Jalview Annotation & T-Coffee Scores
Jalview Features & GFF
Clustal Fasta Pile-Up BLC Stockholm PIR ..etc..
PDBJavascript API
Tight integration with elements on the page
• Selecting• Highlighting• Colours• Scrolling
• Access to Alignment and annotation data
Integrates with Jmol as popup or via javascript messaging
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Jalview comes in two flavours
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VARNAVisual Analysis of RNA
http://jmol.sourceforge.net/ http://varna.lri.fr/
Desktop Structure Visualization3D structures and 2D RNA diagrams
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Clustal Fasta Pile-Up BLC Stockholm PIR ..etc..
Newick & New Hampshire Extended
Jalview Annotation & T-Coffee Scores
Jalview Features & GFF
PDB
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JAVA BIOINFORMATICSANALYSIS
WEB SERVICES
Public services and downloads at www.compbio.dundee.ac.uk/
jabaws/
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The JABAWS Java Client Library
Jalview Web Service GUI
JABAWS command line interface
JABAWSJava Client
JABAWeb Server
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Clustal Fasta Pile-Up BLC Stockholm PIR ..etc..
Newick & New Hampshire Extended
Jalview Annotation & T-Coffee Scores
Jalview Features & GFF
PDB
NEW FOR 2014
MSAprobs: multiple alignment with pair HMMsYongchao Liu, Bertil Schmidt, and Douglas L. Maskell Bioinformatics 2010 26 1958 -1964
GLProbs – adaptive sequence alignmentYongtao Ye et al. Proc. ACM BCB, 2013 pp.152-160http://sourceforge.net/projects/glprobs/
ViennaRNA Ronny Lorenz et al. Algorithms for Molecular Biology, 2011 doi:10.1186/1748-7188-6-26
JPred3Chris Cole, Jon Barber and Geoff BartonNAR Web Server Issue 2008 doi:10.1093/nar/gkn238
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Includes all 3rd party source &
binariesand databases
Reconfigurable parameters,
presets & execution limits
Web UI for installation and status checks
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Released along-side Jalview 2.8.1
on 5th June 2014
New optional downloads:
2.3G Jpred database
Provided as tarball/virtual disk for native and VM installs
http://www.compbio.dundee.ac.uk/jabaws/
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THE JALVIEW 2.8 SERIES
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IT’S (NEARLY) ALL ABOUT STRUCTURE!
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Jalview 2.8 and RNA 2nd-ary Structure
RALEE style colouring highlights distinct stems and
helices
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2.8.1 - Interactive Alignment basedRNA 2nd-ary Structure Prediction
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2.8.1 - Interactive Alignment basedRNA 2nd-ary Structure Prediction
• Shares framework with AACon consensus client
• Predictions update when alignment changes
• settings & results saved in Jalview project
Implemented by our 2013 Summer student
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When ‘partition function’ enabled, the contact probabilities are displayed
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Tooltips provide additional RNAAliFold information
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Protein Secondary Structure Prediction
• Neural network trained on amino acid profiles– Predicts Helix, shEet, or Coil based on sliding
window• Also predicts coiled coils and surface accessibilities
• Server can take– Single Sequence
• Service computes profile with PSI-Blast– Alignment
• Service uses MSA to calculate profile for prediction
SLOW
FAST!
Interactive JPred3 MSA annotation now in 2.8.2 alpha
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2.8.2 alpha - New look Jpred results
Burial now encoded as quantities
Burial and other predictions can be used to colour/filter alignment data
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Secondary structure from 3D data
• Jmol includes a Java port of DSSP– Courtesy of the Vriend
Lab• Jalview 2.8.2 now
employs Jmol to parse PDB data– Display residue level
structure data on sequences
http://jmol.sourceforge.net/
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RNAView, pyRNA
• Fabrice Jossinet’s pyRNA server includes RNAView*
– Identify and characterise base pair interactions in 3D structure
• Used by Jalview to obtain secondary structure for RNA 3D data
* RNAView will shortly be replaced by DSSR (Xiang-Jun Lu)http://x3dna.org/index.php
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• Functionality still to be implemented– Colour sequences by protein as well as RNA
secondary structure– Show/hide per-sequence structure rows– Representative/consensus 2nd-ary structure for a
sequence
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Things I haven’t talked about …
Currently available in v 2.8.1• Internationalisation (Spanish, so far)• View flanking regions (Proteomics)• More score models for PCA/Trees• View ‘representative structures’• Select columns by feature..
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Select column by feature
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Roadmap for Jalview 2.8.2E.T.A September 2014
• Interactive consensus secondary structure annotation for protein alignments– JABA Jpred MSA prediction mode
• Structure based RNA + Protein annotation– Jmol DSSP and XRNA 2.5D
• Prototype Chimera/Jalview interconnect• Feature/Annotation based trees/PCA– Cluster by
• Secondary structure• Displayed sequence annotation
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Michele ClampHarvard & MITUSA.
James CuffHarvard & MITUSA.
The Jalview & JABA Saga
Steve SearleSanger, UK
Andrew WaterhouseU. Basel.
JalviewVersion 22005
JalviewVersion 11997 Jim Procter
(still in Dundee!)
David MartinCLSLT2004
Jalview 1 published.
2009Jalview 2 published
2.1
2.2
2.32.4
2.5 2.6 .1 2.7
Peter TroshinNHS
VAMSAS
Sasha SherstnevGSK
2.8.1
Jalview BBR 2009-2014
JABA BBR ‘13-’18
JABA 1 paper 2011
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Development highlights since 2009New Contributions fromLauren Lui & Jan Engelhart (Google Summer of Code)Anne Menard, Yann Ponty (Paris Sud funding)Paolo Di Tomasso & Natasha SherstnevDavid Roldán Martinez
Thousands of Lines of Code
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2014-2015
The next 5 Years
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And the Saga continues…
Suzanne DuceTraining & OutreachJalview & JABA
Jalview Visual Analytics Scientist/Developers
Alexey DrozdetskiyScientist/Developer
JABA