Large-scale Logging Made Easy: Meetup at Deutsche Bank 2024
Protein and RNA alignment and analysis with Jalview 2.8.2 and JABA 2.1
1. Protein and RNA
alignment and analysis
with Jalview 2.8.2 and JABA 2.1
TT18 and Poster B38
Jim Procter
j.procter@dundee.ac.uk
Jalview Coordinator, Barton Group
College of Life Sciences, University of Dundee, UK.
4. 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
5. Interactive
Editing Visuali zation
Alignments
Structures
Features
Annotation
Tree s
Sequences
PCA
Analysis
Pairwise
alignment
Consensus
Conservation
& Clustering
Shading
Trees/PCA
Newick & New
Hampshire
Extended
Jalview Annotation &
T-Coffee Scores
Jalview Features
& GFF
Clustal Fasta Pile-Up BLC
Stockholm PIR ..etc..
PDB
Javascript 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
9. Clustal Fasta Pile-Up BLC
Stockholm PIR ..etc..
Newick & New
Hampshire
Extended
Jalview Annotation &
T-Coffee Scores
Jalview Features
& GFF
PDB
Distributed
Annotation
System
Interactive
Editing Visuali zation
Alignments
Structures
Features
Annotation
Tree s
Sequences
PCA
Figure
Generation
Clickable
HTML
Clic kable
HTML
Line ArtLine Art
ImagesImages
Analysis
Pairwise
alignment
Consensus
Conservation
& Clustering
Shading
Trees/PCA
11. The JABAWS Java Client Library
Jalview Web
Service GUI
JABAWS command line interface
JABAWS
Java Client
ClustalW
Mafft
Multiple alignmentProtein Disorder Alignment Analysis
JABA
Web Server
12.
13. Clustal Fasta Pile-Up BLC
Stockholm PIR ..etc..
Newick & New
Hampshire
Extended
Jalview Annotation &
T-Coffee Scores
Jalview Features
& GFF
PDB
Distributed
Annotation
System
Interactive
Editing Visuali zation
Alignments
Structures
Features
Annotation
Tree s
Sequences
PCA
Figure
Generation
Clickable
HTML
Clic kable
HTML
Line ArtLine Art
ImagesImages
Analysis
Pairwise
alignment
Consensus
Conservation
& Clustering
Shading
Trees/PCA
NEW FOR 2014
MSAprobs: multiple alignment with pair HMMs
Yongchao Liu, Bertil Schmidt, and Douglas L. Maskell
Bioinformatics 2010 26 1958 -1964
GLProbs – adaptive sequence alignment
Yongtao Ye et al. Proc. ACM BCB, 2013 pp.152-160
http://sourceforge.net/projects/glprobs/
ViennaRNA
Ronny Lorenz et al. Algorithms for Molecular Biology,
2011 doi:10.1186/1748-7188-6-26
JPred3
Chris Cole, Jon Barber and Geoff Barton
NAR Web Server Issue 2008 doi:10.1093/nar/gkn238
14. Native JABAWSinstalls
on arange of platforms
powered by
JABAWSAmazon
Machine Image
on EC2
Includes all 3rd
party source &
binaries
and databases
Reconfigurable
parameters,
presets &
execution limits
Web UI for
installation and
status checks
15. 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/
18. Jalview 2.8 and RNA 2nd-ary Structure
Structure Consensus Logo:
Shows base pair distribution at
each paired position in a given
RNA secondary structure.
Linked VARNA RNA
Secondary Structure
viewer and editor.
RALEE style
colouring highlights
distinct stems and
helices
23. 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
24. 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
25. 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/
26. 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
27. • 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
28. 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..
30. Roadmap for Jalview 2.8.2
E.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
31. Michele Clamp
Harvard & MIT
USA.
James Cuff
Harvard & MIT
USA.
The Jalview & JABA Saga
Steve Searle
Sanger, UK
Andrew Waterhouse
U. Basel.
Jalview
Version 2
2005
Jalview
Version 1
1997
Jim Procter
(still in Dundee!)
David Martin
CLSLT2004
Jalview 1
published.
2009
Jalview 2
published
2.1
2.2
2.3
2.4
2.5 2.6.1 2.7
Peter Troshin
NHS
VAMSAS
Sasha Sherstnev
GSK
2.8.1
Jalview BBR 2009-2014
JABA BBR ‘13-’18
JABA 1 paper
2011
32. Lines of
Code
x10-3
0
200
250
300
2009 2010 2011 2012
2.4.0b2
2.5.1
2.6.1
2.6
2.7
2.8
2.4.0b2
2.5
Development highlights since 2009
ClustalW
Mafft
New Contributions from
Lauren Lui & Jan Engelhart (Google Summer of Code)
Anne Menard, Yann Ponty (Paris Sud funding)
Paolo Di Tomasso & Natasha Sherstnev
David Roldán Martinez
Thousands
of Lines of
Code