The ARB Project

8/2/2019 The ARB Project

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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



! 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



! 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




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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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OTHER

IMPORT Data

LABORATORY


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OTHER

IMPORT Data

LABORATORY

DATABASEQuerying


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Search, Query & Modify ARB DatabaseSearch, Query & Modify ARB Database


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OTHER

IMPORT Data

LABORATORY

DATABASEQuerying


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AutomatedSequence Aligner

PrimaryStructure Editor

SecondaryStructure Editor




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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P i & S d S EdiP i & S d S Edi


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P i & S d St t EditP i & S d St t Edit


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OTHER

IMPORT Data

LABORATORY

DATABASEQuerying



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Phylogenetic

Treeing







OTHER

IMPORT Data

LABORATORY

DATABASEQuerying

1

1 2 3 4

0 3 5 5

1 2 3 4 5 6 7

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

2

3

4

3

42

Phylogenetic Tree BuildingMethods

Phenetic Methods Cladistic Methods

Character BasedDistance based

1

3

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Maximum LikelihoodMethod

Neighbor JoiningMethod

Maximum ParsimonyMethodMinimum EvolutionMethod

1

1 2 3 4

0 3 5 5

1 2 3 4 5 6 7

T T A T T A A11

1


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234

0 4 40 2

0

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

2

3

4

3

42

Phylogenetic Tree BuildingMethods

Phenetic Methods Cladistic Methods

Character BasedDistance based

1

3

42

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


Selects the tree whose sum of branch

lengths is the minimum


Selects the tree that require fewer

evolutionary changes


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Treeing Methods inARB

Parsimony Method

1

3

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1

3

42

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

3

4

Neighbor Joining

MethodFastDNAml Method

Distance Based Character Based

Phylip Distance MatrixMethod

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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



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Phylogenetic

Treeing






OTHER

IMPORT Data

LABORATORY

DATABASEQuerying



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Phylogenetic

Treeing






OTHER

IMPORT Data

LABORATORY

DATABASEQuerying

Visualization ofSequence Data

Visualization of Sequence DataVisualization of Sequence Data


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sua at o o Seque ce ataq



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qq



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Phylogenetic

Treeing






OTHER

IMPORT Data

LABORATORY

DATABASEQuerying




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Phylogenetic

Treeing

Positional TreeSERVER

Probe Match Probe Design






OTHER

IMPORT Data

LABORATORY

DATABASEQuerying


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


OTHERLABORATORY


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Phylogenetic

Treeing








OTHER

IMPORT Data

LABORATORY

DATABASEQuerying



OTHERLABORATORY GCG

GENBANK

OTHER

FASTA

EBI


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Phylogenetic

Treeing

Further Analysis / Laboratory /Storage / Printing








OTHER

IMPORT Data

LABORATORY GCG OTHEREBI

EXPORT Data

DATABASEQuerying


The ARB Genome Project


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j

EXPERIMENT ORGANISM

GENES



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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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EXPERIMENT ORGANISM

GENES



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EXPERIMENT ORGANISM

GENES



Probe & PrimerDesign

Automated Aligner

Searching for Genes in the Genome of Organisms and displaying respectiveGene Information


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ORGANISM



EXPERIMENT

GENES




Automated Aligner



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ORGANISM




Analysed Data Results Protocols

GENES




Automated Aligner

EXPERIMENT

Experiment Data Entry Form


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ORGANISM





GENES




Automated Aligner

EXPERIMENT



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ORGANISM





GENES




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

The ARB Project

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Transcript of The ARB Project