protein and rna alignment and analysis with jalview 2.8.2 and jaba 2.1

Protein and RNAalignment and analysis

with Jalview 2.8.2 and JABA 2.1

TT18 and Poster B38Jim Procter

j.procter@dundee.ac.ukJalview Coordinator, Barton Group

College of Life Sciences, University of Dundee, UK.

Standalone or web based

Java

alignmentviewerand

editor&

annotation, tree, and structure

Available at www.jalview.or

g

One alignment, many views

Sequence features highlight key regions like functional sites

Alignment annotation area shows graphs and symbols from

calculations and manual curation

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

Newick & New Hampshire Extended

Jalview Annotation & T-Coffee Scores

Jalview Features & GFF

Clustal Fasta Pile-Up BLC Stockholm PIR ..etc..

PDBJavascript 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

Jalview comes in two flavours

VARNAVisual Analysis of RNA

http://jmol.sourceforge.net/ http://varna.lri.fr/

Desktop Structure Visualization3D structures and 2D RNA diagrams

Clustal Fasta Pile-Up BLC Stockholm PIR ..etc..

Newick & New Hampshire Extended

Jalview Annotation & T-Coffee Scores

Jalview Features & GFF

PDB

JAVA BIOINFORMATICSANALYSIS

WEB SERVICES

Public services and downloads at www.compbio.dundee.ac.uk/

jabaws/

The JABAWS Java Client Library

Jalview Web Service GUI

JABAWS command line interface

JABAWSJava Client

JABAWeb Server

Clustal Fasta Pile-Up BLC Stockholm PIR ..etc..

Newick & New Hampshire Extended

Jalview Annotation & T-Coffee Scores

Jalview Features & GFF

PDB

NEW FOR 2014

MSAprobs: multiple alignment with pair HMMsYongchao Liu, Bertil Schmidt, and Douglas L. Maskell Bioinformatics 2010 26 1958 -1964

GLProbs – adaptive sequence alignmentYongtao Ye et al. Proc. ACM BCB, 2013 pp.152-160http://sourceforge.net/projects/glprobs/

ViennaRNA Ronny Lorenz et al. Algorithms for Molecular Biology, 2011 doi:10.1186/1748-7188-6-26

JPred3Chris Cole, Jon Barber and Geoff BartonNAR Web Server Issue 2008 doi:10.1093/nar/gkn238

Includes all 3rd party source &

binariesand databases

Reconfigurable parameters,

presets & execution limits

Web UI for installation and status checks

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/

THE JALVIEW 2.8 SERIES

IT’S (NEARLY) ALL ABOUT STRUCTURE!

Jalview 2.8 and RNA 2nd-ary Structure

RALEE style colouring highlights distinct stems and

helices

2.8.1 - Interactive Alignment basedRNA 2nd-ary Structure Prediction

2.8.1 - Interactive Alignment basedRNA 2nd-ary Structure Prediction

• Shares framework with AACon consensus client

• Predictions update when alignment changes

• settings & results saved in Jalview project

Implemented by our 2013 Summer student

When ‘partition function’ enabled, the contact probabilities are displayed

Tooltips provide additional RNAAliFold information

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

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

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/

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

• 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

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..

Select column by feature

Roadmap for Jalview 2.8.2E.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

Michele ClampHarvard & MITUSA.

James CuffHarvard & MITUSA.

The Jalview & JABA Saga

Steve SearleSanger, UK

Andrew WaterhouseU. Basel.

JalviewVersion 22005

JalviewVersion 11997 Jim Procter

(still in Dundee!)

David MartinCLSLT2004

Jalview 1 published.

2009Jalview 2 published

2.1

2.2

2.32.4

2.5 2.6 .1 2.7

Peter TroshinNHS

VAMSAS

Sasha SherstnevGSK

2.8.1

Jalview BBR 2009-2014

JABA BBR ‘13-’18

JABA 1 paper 2011

Development highlights since 2009New Contributions fromLauren Lui & Jan Engelhart (Google Summer of Code)Anne Menard, Yann Ponty (Paris Sud funding)Paolo Di Tomasso & Natasha SherstnevDavid Roldán Martinez

Thousands of Lines of Code

2014-2015

The next 5 Years

And the Saga continues…

Suzanne DuceTraining & OutreachJalview & JABA

Jalview Visual Analytics Scientist/Developers

Alexey DrozdetskiyScientist/Developer

JABA