jalview 2.9.x series roadmap (bivi 2015, norwich, uk)

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  ?