Jalview 2.9.x series roadmap (BiVi 2015, Norwich, UK)

•

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A brief but intense overview of the features to look forward to in the Jalview 2.9.x series being developed in 2016, and some preliminary work on visualising sequence search results.

Science

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

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

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

The
PDBe
REST
API

hUp://www.ebi.ac.uk/pdbe/pdbe-‐rest-‐api

Includes
REST
endpoints

backed
by
Apache
SOLR

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
Interactive
Editing Visualization
Alignments
Structures
Features
Annotation
Trees
Sequences
PCA
Figure
Generation
Clickable
HTML
Clickable
HTML
Line ArtLine Art
ImagesImages
Analysis
Pairwise
alignment
Consensus
Conservation
& Clustering
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
Hit4
Hit2
Hit1
Hit5
Hit3
a
Query
Hit4
Hit2
Hit1
Hit5
Hit3
b
Query
Hit4
Hit2
Hit1
Hit5
Hit3
c
Figure
adapted
from

Procter
et
al.
(2010)
Nature
Methods
7
S16
-‐
S25

Database
Search
and
opPmal
MSAs

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
?

This document provides an overview of the Jalview 2.8.2 and JABA 2.1 software for protein and RNA alignment analysis. Key features include an interactive Java alignment viewer and editor, integrated structure viewers, and predictive annotation of secondary structure. Upcoming updates focus on consensus-based RNA structure prediction and utilizing 3D structural data for protein and RNA annotation directly in the alignment. The software continues to be developed and maintained by the Barton Group at the University of Dundee.

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Jalview 2.9.x series roadmap (BiVi 2015, Norwich, UK)

1. JALVIEW 2.9… WHERE ARE WE GOING ? JIM PROCTER, JALVIEW COORDINATOR, UNIVERSITY OF DUNDEE www.jalview.org supported)by

2. 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

3. The web was where Jalview started hUp://pfam.xfam.org/family/bromodomain#tabview=tab3

4. Illustrator Word/LaTeX.. Etc... Google Alignment on Web Jalview

5. 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

6. PUBLISHING ALIGNMENTS

7. Export dialog Msaviewer publicaPon Yachdav et al. 2015 hUp://dx.doi.org/10.7554/eLife.07009

8. HTML output – based on SVG Sliders scroll around alignment

9. SVG – From JFreeChart’s SVG library •  Vfwvf

10.

11.

12. HTML publishing in Jalview •  HTML ﬁles can re-‐imported – ‘BioJSON’ represents a Jalview view – Speciﬁed as JSONSchema •  Publishing opPons – Scrollable SVG – BioJS MSA Viewer

13. Jalview and the BioJS-‐MSA viewer Msaviewer publicaPon Yachdav et al. 2015 hUp://dx.doi.org/10.7554/eLife.07009

14. MULTIPLE COORDINATED AND INTEGRATED VIEWS

15. 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

16. Group selec+ons Edits mouseovers Integrated Coding/Product view

17. SOURCES OF CODING DATA

18. Annotated ConPgs, cDNA and products •  Drag and drop cDNA or Protein products

19. µ Annotated ConPgs, cDNA and products 3D Structures of Macromolecules Annotated Protein Domain Alignments Annotated RNA Domain Alignments Annotated Protein Sequences

20. NEW PDB STRUCTURE UI

21. The PDBe REST API hUp://www.ebi.ac.uk/pdbe/pdbe-‐rest-‐api Includes REST endpoints backed by Apache SOLR

22. Jalview’s new PDBe dialog in 2.9

23. View 3D Structure … •  Unusable for “Popular Structures” •  PDBe SOLR interface allows ‘best’ structures to be picked

24. interesPng structures for alignment in 2.9

25. Jmol and Chimera •  Colour by alignment •  SuperposiPon •  Mouseovers •  Session storage Jalview <> Chimera via HTTP REST API Also see Chimera selecSons highlighted in Jalview

26. Clustal Fasta Pile-‐Up BLC Stockholm PIR ..etc.. Newick & New Hampshire Extended Jalview AnnotaPon & T-‐Coﬀee Scores Jalview Features & GFF PDB Distributed Annotation System Interactive Editing Visualization Alignments Structures Features Annotation Trees Sequences PCA Figure Generation Clickable HTML Clickable HTML Line ArtLine Art ImagesImages Analysis Pairwise alignment Consensus Conservation & Clustering Shading Trees/PCA

27. WOT NO SEQUENCE SEARCH! Probably the biggest reason why people don’t use Jalview….

28. 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

29. Query Hit4 Hit2 Hit1 Hit5 Hit3 a Query Hit4 Hit2 Hit1 Hit5 Hit3 b Query Hit4 Hit2 Hit1 Hit5 Hit3 c Figure adapted from Procter et al. (2010) Nature Methods 7 S16 -‐ S25 Database Search and opPmal MSAs

30. HMMER3 EMBL-‐EBI Server

31. HMMER3 EMBL-‐EBI Server

32. HMMER3 EMBL-‐EBI Server

33. Gerng data from HMMER3

34.

35.

36. Bad VIS Encodings QuanPPes as Hue and Transparency

37. Challenge: Jalview should complement HMMER Web Interface

38. Training videos covering all the basics hUp://youtu.be/pKs0aMUSW0 hUp://youtu.be/JFXUfq-‐Sjts hUp://youtu.be/RdbcdZZUDHg QuesSons ?