jalview 2.9.x series roadmap (bivi 2015, norwich, uk)
TRANSCRIPT
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JALVIEW 2.9… WHERE ARE WE GOING ?
JIM PROCTER, JALVIEW COORDINATOR, UNIVERSITY OF DUNDEE
www.jalview.org
supported)by
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The Jalview and Dundee Protein Resource Core Team
Tochukwu (Charles) Ofoegbu
Alexey Drozdetskiy Protein predicPon
and analysis services
Mungo Carstairs
Suzanne Duce Jalview & Dundee Protein Resource
Geoff Barton
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The web was where Jalview started
hUp://pfam.xfam.org/family/bromodomain#tabview=tab3
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Illustrator Word/LaTeX.. Etc...
Google Alignment on Web
Jalview
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One alignment, many views
Sequence features on sequences shown to
highlighted key regions
Alignment annotaPon area shows graphs and symbols from
calculaPons and manual curaPon
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PUBLISHING ALIGNMENTS
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Export dialog
Msaviewer publicaPon Yachdav et al. 2015 hUp://dx.doi.org/10.7554/eLife.07009
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HTML output – based on SVG
Sliders scroll around alignment
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SVG – From JFreeChart’s SVG library
• Vfwvf
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HTML publishing in Jalview
• HTML files can re-‐imported – ‘BioJSON’ represents a Jalview view – Specified as JSONSchema
• Publishing opPons – Scrollable SVG – BioJS MSA Viewer
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Jalview and the BioJS-‐MSA viewer
Msaviewer publicaPon Yachdav et al. 2015 hUp://dx.doi.org/10.7554/eLife.07009
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MULTIPLE COORDINATED AND INTEGRATED VIEWS
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Linked Jmol viewer shows one or more
structures coloured by alignment
Linked tree viewer allows subgroups to be idenPfied in alignment
Group selec+ons
Colours and mouseovers
MulPple coordinated views
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Group selec+ons
Edits mouseovers
Integrated Coding/Product view
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SOURCES OF CODING DATA
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Annotated ConPgs, cDNA and products
• Drag and drop cDNA or Protein products
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µ Annotated ConPgs, cDNA
and products
3D Structures of Macromolecules
Annotated Protein Domain Alignments
Annotated RNA Domain Alignments
Annotated Protein Sequences
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NEW PDB STRUCTURE UI
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The PDBe REST API hUp://www.ebi.ac.uk/pdbe/pdbe-‐rest-‐api
Includes REST endpoints backed by Apache SOLR
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Jalview’s new PDBe dialog in 2.9
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View 3D Structure …
• Unusable for “Popular Structures”
• PDBe SOLR interface allows ‘best’ structures to be picked
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interesPng structures for alignment in 2.9
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Jmol and Chimera • Colour by alignment • SuperposiPon • Mouseovers • Session storage
Jalview <> Chimera via HTTP REST API Also see Chimera selecSons highlighted in Jalview
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Clustal Fasta Pile-‐Up BLC Stockholm PIR ..etc..
Newick & New Hampshire Extended
Jalview AnnotaPon & T-‐Coffee Scores
Jalview Features & GFF
PDB
Distributed Annotation System
In t er a c t i v e E d i t i n g V i su ali z a t i on
A li gn m e n t s
S t r u c t u re s
Fe a t u re s
A nn o t a t i on
T ree s
Se qu e n c e s
P C A
F i gu r e Ge n er a t i on
C lic k a b l e H TM L C lic k a b l e H TM L L i n e A r t L i n e A r t
I m a g e s I m a g e s
A n al y s i s Pairwise
alignment
C on se n s u s C on se r v a t io n & C lu s t er in g
Shading
Trees/PCA
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WOT NO SEQUENCE SEARCH! Probably the biggest reason why people don’t use Jalview….
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Sequence • Could also be a sequence profile
Align against sequence database
• Database (size-‐>stats)
• Score model
Significant hits aligned to query
• Bit score • E-‐Value
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Query
Hit4Hit2
Hit1
Hit5
Hit3
aQuery
Hit4Hit2
Hit1
Hit5
Hit3
bQuery
Hit4Hit2
Hit1
Hit5
Hit3
c
Figure adapted from Procter et al. (2010) Nature Methods 7 S16 -‐ S25
Database Search and opPmal MSAs
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HMMER3 EMBL-‐EBI Server
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HMMER3 EMBL-‐EBI Server
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HMMER3 EMBL-‐EBI Server
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Gerng data from HMMER3
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Bad VIS Encodings QuanPPes as Hue and Transparency
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Challenge: Jalview should complement HMMER Web Interface
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Training videos covering all the basics
hUp://youtu.be/pKs0aMUSW0
hUp://youtu.be/JFXUfq-‐Sjts hUp://youtu.be/RdbcdZZUDHg QuesSons ?