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The ARB Project
An integrated, non-commercial software solutionfor Phylogenetic Treeing, Sequence Data Analysis
and Molecular Probe Design
Presentation by Yadhu Kumar, ARB Group
Le h r st u h l f r M ik r o b i o l og i e
Leh rs tu h l f r Rechne r t echn i k & Rechne ro r gan i sa t i on
Techn ische Un ive r s i t t Mnchen , Mnchen , Germ any
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Ideas
! Central Database to maintain a structured integrativesecondary data in combination with processed primary structures
(aligned sequences) and any additional data assigned to theindividual sequences.
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Ideas
! Central Database to maintain a structured integrativesecondary data in combination with processed primary structures
(aligned sequences) and any additional data assigned to theindividual sequences.
! Comprehensive selection of software tools directly interactingwith one another and as well as with the central databasefacilitating in depth analysis of molecular data.
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Ideas
! Central Database to maintain a structured integrativesecondary data in combination with processed primary structures
(aligned sequences) and any additional data assigned to theindividual sequences.
! Comprehensive selection of software tools directly interactingwith one another and as well as with the central databasefacilitating in depth analysis of molecular data.
! Common Graphical User Interface
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ARB DATABASEAligned Sequences, Descriptive
Data, User Data, Profiles,Filters, Trees
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EBI / GENBANK / RDP / ANTWERPEN
OTHER
IMPORT Data
LABORATORY
ARB DATABASEAligned Sequences, Descriptive
Data, User Data, Profiles,Filters, Trees
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ARB Main Window & Import WindowARB Main Window & Import Window
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ARB Main Window & Import WindowARB Main Window & Import Window
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ARB DATABASEAligned Sequences, Descriptive
Data, User Data, Profiles,Filters, Trees
EBI / GENBANK / RDP / ANTWERPEN
OTHER
IMPORT Data
LABORATORY
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ARB DATABASEAligned Sequences, Descriptive
Data, User Data, Profiles,Filters, Trees
EBI / GENBANK / RDP / ANTWERPEN
OTHER
IMPORT Data
LABORATORY
DATABASEQuerying
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Search, Query & Modify ARB DatabaseSearch, Query & Modify ARB Database
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Search, Query & Modify ARB DatabaseSearch, Query & Modify ARB Database
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Search, Query & Modify ARB DatabaseSearch, Query & Modify ARB Database
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ARB DATABASEAligned Sequences, Descriptive
Data, User Data, Profiles,Filters, Trees
EBI / GENBANK / RDP / ANTWERPEN
OTHER
IMPORT Data
LABORATORY
DATABASEQuerying
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AutomatedSequence Aligner
PrimaryStructure Editor
SecondaryStructure Editor
ARB DATABASEAligned Sequences, Descriptive
Data, User Data, Profiles,Filters, Trees
EBI / GENBANK / RDP / ANTWERPEN
OTHER
IMPORT Data
LABORATORY
ClustalW
Fast Aligner
DATABASEQuerying
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Primary & Secondary Structure EditorsPrimary & Secondary Structure Editors
S S
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Primary & Secondary Structure EditorsPrimary & Secondary Structure Editors
P i & S d S EdiP i & S d S Edi
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Primary & Secondary Structure EditorsPrimary & Secondary Structure Editors
P i & S d St t EditP i & S d St t Edit
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Primary & Secondary Structure EditorsPrimary & Secondary Structure Editors
EBI / GENBANK / RDP / ANTWERPEN
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AutomatedSequence Aligner
PrimaryStructure Editor
SecondaryStructure Editor
ARB DATABASEAligned Sequences, Descriptive
Data, User Data, Profiles,Filters, Trees
EBI / GENBANK / RDP / ANTWERPEN
OTHER
IMPORT Data
LABORATORY
DATABASEQuerying
EBI / GENBANK / RDP / ANTWERPEN
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Phylogenetic
Treeing
AutomatedSequence Aligner
PrimaryStructure Editor
SecondaryStructure Editor
ARB DATABASEAligned Sequences, Descriptive
Data, User Data, Profiles,Filters, Trees
EBI / GENBANK / RDP / ANTWERPEN
OTHER
IMPORT Data
LABORATORY
DATABASEQuerying
1
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T T A T T A A11
1
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1234
0 3 5 50 4 4
0 20
T T A T T A A
A A T T T A A
A A A A A T A
A A A A A A T
1
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Phylogenetic Tree BuildingMethods
Phenetic Methods Cladistic Methods
Character BasedDistance based
1
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Maximum LikelihoodMethod
Neighbor JoiningMethod
Maximum ParsimonyMethodMinimum EvolutionMethod
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1 2 3 4 5 6 7
T T A T T A A11
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0 4 40 2
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T T A T T A A
A A T T T A A
A A A A A T A
A A A A A A T
1
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Phylogenetic Tree BuildingMethods
Phenetic Methods Cladistic Methods
Character BasedDistance based
1
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Maximum LikelihoodMethod
Neighbor JoiningMethod
Clustering Algorithm
Builds a small tree and keeps adding thesequences to arrive at a full desired tree
Optimality Criterion
Selects the tree that is most likely tohave produced the observed data
Maximum ParsimonyMethodMinimum EvolutionMethod
Optimality Criterion
Selects the tree whose sum of branch
lengths is the minimum
Optimality Criterion
Selects the tree that require fewer
evolutionary changes
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Treeing Methods inARB
Parsimony Method
1
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1
3
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1 2 3 4 5 6 7
T T A T T A A
A A T T T A A
A A A A A T AA A A A A A T
1
2
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Neighbor Joining
MethodFastDNAml Method
Distance Based Character Based
Phylip Distance MatrixMethod
123
4
1 2 3 4
0 3 5 50 4 4
0 2
0
The ARB Parsimony ToolThe ARB Parsimony Tool
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The ARB Parsimony ToolThe ARB Parsimony Tool
" Able to handle bigtrees (e.g. >30.00016S/18S rRNA
sequences)
" Allows optimizationof trees and sub-trees with different
parameters.
" Adding sequencesis possible without
changing initialtopology.
Phylogenetic Treeing using ARB SoftwarePhylogenetic Treeing using ARB Software
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Phylogenetic Treeing using ARB SoftwarePhylogenetic Treeing using ARB Software
Import Sequences
Alignment of Sequenceswith Automated Aligner
Manual Correction ofAligned Sequences
Primary StructureEditor SecondaryStructure Editor
Phylogenetic
Treeing
Visualization andInference of Trees
EBI / GENBANK / RDP / ANTWERPEN
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Phylogenetic
Treeing
AutomatedSequence Aligner
PrimaryStructure Editor
SecondaryStructure Editor
ARB DATABASEAligned Sequences, Descriptive
Data, User Data, Profiles,Filters, Trees
OTHER
IMPORT Data
LABORATORY
DATABASEQuerying
EBI / GENBANK / RDP / ANTWERPEN
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Phylogenetic
Treeing
AutomatedSequence Aligner
PrimaryStructure Editor
SecondaryStructure Editor
ARB DATABASEAligned Sequences, Descriptive
Data, User Data, Profiles,Filters, Trees
OTHER
IMPORT Data
LABORATORY
DATABASEQuerying
Visualization ofSequence Data
Visualization of Sequence DataVisualization of Sequence Data
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Visualization of Sequence DataVisualization of Sequence Data
Visualization of Sequence DataVisualization of Sequence Data
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Visualization of Sequence DataVisualization of Sequence Data
Visualization of Sequence DataVisualization of Sequence Data
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sua at o o Seque ce ataq
Visualization of Sequence DataVisualization of Sequence Data
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EBI / GENBANK / RDP / ANTWERPEN
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Phylogenetic
Treeing
AutomatedSequence Aligner
PrimaryStructure Editor
SecondaryStructure Editor
ARB DATABASEAligned Sequences, Descriptive
Data, User Data, Profiles,Filters, Trees
OTHER
IMPORT Data
LABORATORY
DATABASEQuerying
Visualization ofSequence Data
EBI / GENBANK / RDP / ANTWERPEN
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Phylogenetic
Treeing
Positional TreeSERVER
Probe Match Probe Design
AutomatedSequence Aligner
PrimaryStructure Editor
SecondaryStructure Editor
ARB DATABASEAligned Sequences, Descriptive
Data, User Data, Profiles,Filters, Trees
OTHER
IMPORT Data
LABORATORY
DATABASEQuerying
Visualization ofSequence Data
Probe Design and Probe MatchProbe Design and Probe Match
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Probe Design and Probe MatchProbe Design and Probe Match
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Probe Design and Probe MatchProbe Design and Probe Match
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Probe Design and Probe MatchProbe Design and Probe Match
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Combination of the Protargol Method according toCombination of the Protargol Method according to
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Combination of the Protargol Method according toCombination of the Protargol Method according to
Foissner with FISH onFoissner with FISH on EpistylisEpistylissp
28 m
sp
Under Light Microscope Under Fluorescent Microscope
Pictures from Dr. Johannes Fried
H b idi d DNA ChiH b idi d DNA Chi
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Hybridised DNA ChipsHybridised DNA Chips
E. sulfureus
T. halophilus
E. asini
E
nc3
as0
8i
E
nc38
su18
Tha09
UB3i
EE
UB338
nc38i
ssa3
mprs
asu5
soha5
eCo
E
neu
E
a
8
E
a
09
E
s
8i
E
7
E
9
E
38
-v
ntrol
DNA chip images from Dr. Thomas Behr
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Design of multiple probes forDesign of multiple probes for GlaucomaGlaucoma scintillansscintillans
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Design of multiple probes forDesign of multiple probes for GlaucomaGlaucomascintillansscintillans
In situ hybridization ofIn situ hybridization of GlaucomaGlaucomascintillansscintillanswithwith
multiple probesmultiple probes
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20 m
A B
DC
20 m
A B
DC
multiple probesmultiple probes
B : Genus SpecificProbe 1
A : SpeciesSpecific Probe
C : Genus SpecificProbe 2
D : G. scintillans
under lightmicroscope
Pictures from Dr. Johannes Fried
EBI / GENBANK / RDP / ANTWERPEN
OTHERLABORATORY
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Phylogenetic
Treeing
Positional TreeSERVER
Probe Match Probe Design
AutomatedSequence Aligner
PrimaryStructure Editor
SecondaryStructure Editor
ARB DATABASEAligned Sequences, Descriptive
Data, User Data, Profiles,Filters, Trees
OTHER
IMPORT Data
LABORATORY
DATABASEQuerying
Visualization ofSequence Data
EBI / GENBANK / RDP / ANTWERPEN
OTHERLABORATORY GCG
GENBANK
OTHER
FASTA
EBI
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Phylogenetic
Treeing
Further Analysis / Laboratory /Storage / Printing
Positional TreeSERVER
Probe Match Probe Design
AutomatedSequence Aligner
PrimaryStructure Editor
SecondaryStructure Editor
ARB DATABASEAligned Sequences, Descriptive
Data, User Data, Profiles,Filters, Trees
OTHER
IMPORT Data
LABORATORY GCG OTHEREBI
EXPORT Data
DATABASEQuerying
Visualization ofSequence Data
The ARB Genome Project
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j
EXPERIMENT ORGANISM
GENES
The ARB Genome Project
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j
Descriptive Data Database Query
SequencesMapsImport Filters
EXPERIMENT ORGANISM
GENES
ARB Genome Window : Displaying List of Organisms and associated information
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Genome map of Listeria monocytogenesdisplaying rRNA Operons
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Genome map in block view and Individual Gene Information display
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The ARB Genome Project
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Descriptive Data Database Query
SequencesMapsImport Filters
EXPERIMENT ORGANISM
GENES
The ARB Genome Project
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Descriptive Data Database Query
SequencesMapsImport Filters
EXPERIMENT ORGANISM
GENES
Descriptive Data Database Query
PrimaryStructure Editor
Probe & PrimerDesign
Automated Aligner
Searching for Genes in the Genome of Organisms and displaying respectiveGene Information
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The ARB Genome Project
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ORGANISM
Descriptive Data Database Query
SequencesMapsImport Filters
EXPERIMENT
GENES
Descriptive Data Database Query
PrimaryStructure Editor
Probe & PrimerDesign
Automated Aligner
The ARB Genome Project
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ORGANISM
Descriptive Data Database Query
SequencesMapsImport Filters
Descriptive Data Database Query
Analysed Data Results Protocols
GENES
Descriptive Data Database Query
PrimaryStructure Editor
Probe & PrimerDesign
Automated Aligner
EXPERIMENT
Experiment Data Entry Form
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The ARB Genome Project
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ORGANISM
Descriptive Data Database Query
SequencesMapsImport Filters
Descriptive Data Database Query
Analysed Data Results Protocols
GENES
Descriptive Data Database Query
PrimaryStructure Editor
Probe & PrimerDesign
Automated Aligner
EXPERIMENT
The ARB Genome Project
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ORGANISM
Descriptive Data Database Query
SequencesMapsImport Filters
Descriptive Data Database Query
Analysed Data Results Protocols
GENES
Descriptive Data Database Query
PrimaryStructure Editor
Probe & PrimerDesign
Automated Aligner
EXPERIMENT
PHYSIOLOGICALPATHWAYS
Currently Maintained ARB DatabasesCurrently Maintained ARB Databases
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Currently Maintained ARB DatabasesCurrently Maintained ARB Databases
(Eucarya, Archaea, Bacteria)(Eucarya, Archaea, Bacteria)
# Small subunit rRNA 16S,18S rRNA (41,737)# Large subunit rRNA 23S, 28S rRNA (7,312)
# Elongation initiation factors
# Proton translocation ATPase subunits
# Heat shock proteins
# recA
# RNA polymerases
#DNA gyrase
# Cytochromeoxidase
External Communication
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Operating Systems
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Programming Languages
! C, C++, Perl and other scripting languages
! GUI is based on X Windows & Open Motif Library
LINUX / UnixOperating System
Mac OS ?
ARB running on Vmware, a Linux emulation software under Windows
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Operating Systems
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Programming Languages
! C, C++, Perl and other scripting languages
! GUI is based on X Windows & Open Motif Library
LINUX / UnixOperating System
Mac OS ?
Availability & Documentation
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www.arb-home.de
A s w e e n j o y g r e a t A d v an ta g e s f r o m
th e I n v e n t i o n s of o t h e r s , w e s h o u l dbe g lad o f an Oppor t un i t y to se rveo th e r s b y a n y I n v e n t i o n o f o u r s ; an dth i s w e shou ld do f r ee ly andgenerous l y . ' '
- B en j a m i n Fr a n k li n
People Behind The ARB Project
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Group Leader
Dr. Wolfgang Ludwig
Lehrstuhl fuer MikrobiologieTechnische Universitaet [email protected]
Programmers and Curators
O.Strunk, R.Westram, L. Richter, H. Meier, Yadhukumar,A.Buchner, T.Lai, G.Jobb, S.Steppi, W. Frster, H. May, S.Hermann, N. Stuckmann, O. Gross, B. Nonhoff, R. Jost, B.
Reichel,T. Ginhart, A. Vilbig, T. Liss, M. Lenke,
Future Goals
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! Online Probe Design using ARB Positional Tree server
! Multiple probe sets for selected phylogenetic groups(chip design)
! Chip data analysis and evaluation tool
! Further Development of ARB Genome Analysis Software
!
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Thank You
Presentation by Yadhu Kumar, ARB Group