jalview 2.9.x series roadmap (bivi 2015, norwich, uk)
TRANSCRIPT
JALVIEW 2.9… WHERE ARE WE GOING ?
JIM PROCTER, JALVIEW COORDINATOR, UNIVERSITY OF DUNDEE
www.jalview.org
supported)by
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
The web was where Jalview started
hUp://pfam.xfam.org/family/bromodomain#tabview=tab3
Illustrator Word/LaTeX.. Etc...
Google Alignment on Web
Jalview
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
PUBLISHING ALIGNMENTS
Export dialog
Msaviewer publicaPon Yachdav et al. 2015 hUp://dx.doi.org/10.7554/eLife.07009
HTML output – based on SVG
Sliders scroll around alignment
SVG – From JFreeChart’s SVG library
• Vfwvf
HTML publishing in Jalview
• HTML files can re-‐imported – ‘BioJSON’ represents a Jalview view – Specified as JSONSchema
• Publishing opPons – Scrollable SVG – BioJS MSA Viewer
Jalview and the BioJS-‐MSA viewer
Msaviewer publicaPon Yachdav et al. 2015 hUp://dx.doi.org/10.7554/eLife.07009
MULTIPLE COORDINATED AND INTEGRATED VIEWS
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
Group selec+ons
Edits mouseovers
Integrated Coding/Product view
SOURCES OF CODING DATA
Annotated ConPgs, cDNA and products
• Drag and drop cDNA or Protein products
µ Annotated ConPgs, cDNA
and products
3D Structures of Macromolecules
Annotated Protein Domain Alignments
Annotated RNA Domain Alignments
Annotated Protein Sequences
NEW PDB STRUCTURE UI
The PDBe REST API hUp://www.ebi.ac.uk/pdbe/pdbe-‐rest-‐api
Includes REST endpoints backed by Apache SOLR
Jalview’s new PDBe dialog in 2.9
View 3D Structure …
• Unusable for “Popular Structures”
• PDBe SOLR interface allows ‘best’ structures to be picked
interesPng structures for alignment in 2.9
Jmol and Chimera • Colour by alignment • SuperposiPon • Mouseovers • Session storage
Jalview <> Chimera via HTTP REST API Also see Chimera selecSons highlighted in Jalview
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
WOT NO SEQUENCE SEARCH! Probably the biggest reason why people don’t use Jalview….
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
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
HMMER3 EMBL-‐EBI Server
HMMER3 EMBL-‐EBI Server
HMMER3 EMBL-‐EBI Server
Gerng data from HMMER3
Bad VIS Encodings QuanPPes as Hue and Transparency
Challenge: Jalview should complement HMMER Web Interface
Training videos covering all the basics
hUp://youtu.be/pKs0aMUSW0
hUp://youtu.be/JFXUfq-‐Sjts hUp://youtu.be/RdbcdZZUDHg QuesSons ?