Aligning Kinases

Aligning KinasesApplying MSA Analysis to the CDK family

Building A Multiple Sequence Alignment

Potential Uses of A Multiple Sequence Alignment?

chite ---ADKPKRPLSAYMLWLNSARESIKRENPDFK-VTEVAKKGGELWRGLKDwheat --DPNKPKRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSEtrybr KKDSNAPKRAMTSFMFFSSDFRS----KHSDLS-IVEMSKAAGAAWKELGPmouse -----KPKRPRSAYNIYVSESFQ----EAKDDS-AQGKLKLVNEAWKNLSP ***. ::: .: .. . : . . * . *: *

chite AATAKQNYIRALQEYERNGG-wheat ANKLKGEYNKAIAAYNKGESAtrybr AEKDKERYKREM---------mouse AKDDRIRYDNEMKSWEEQMAE * : .* . : ExtrapolationMotifs/PatternsPhylogenyProfilesStruc. PredictionMultiple Alignments Are CENTRAL to MOST Bioinformatics Techniques.

1

Organizing a Family GatheringThe CDK example

Choosing the Right SequencesSwisProtLitteratureOther Databases

Organizing the DataSRSPublic DataIGS DataAventisCDKGenecardManualAutomatic

Accessing the Data: The Fischer ServerFischer will ContainA collection of Flat filesA secure SRS serverFile Formats

The server is a Technology PipelineCan be adapted in real timeCan be Transfered

Our CDK DataCDKs and CDK-likeProtein InformationFunctional FeaturesStructural Information

Genomic InformationGenesVariantSNPs

Our MSA dataset29 amino acid sequences (CDKS and Aurora families, stemming from primary transcripts)2 isoforms of a cdk member 4 PDB structures : 1MUO (AUR A) 1BLX (CDK 6 ) 1b38 (CDK 2) 1H4L (CDK 5)

Use of T-coffee release 1.78 with integration of the structure informations contained in pdb files

2

Aligning The Sequences

Building A Multiple Sequence AlignmentClustalWT-CoffeeMuscleHand EditingCombinationComparison

Using Structural Information3D-CoffeeStruct Vs StructSeq Vs StructThreadSuperposeSeq Vs SeqLocal Global

Method

Accessing the Methods:FischerPublic 3D-Coffee serverigs-server.cnrs-mrs.fr/TCoffee/

FischerLatest version of T-CoffeeCustomised parametersCoktails of MSA methods

3

Dressing Up aMultiple Sequence Alignment

Feature Dressing-25 Binding site-20 Phospho-40 nsSNP-50 Splice SiteEscript

Feature Dressing

4

How Good Is The Alignment

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T-Coffee CORE Evaluation

T-Coffee CORE Evaluation

CORE indexSpecificity () and Sensitivity ()

Feature Based Evaluation

Features mapping on multiple alignmentT-coffeeClustalW

Structure Based EvaluationAPDB

Structure Based EvaluationAPDB

Structure Based EvaluationAPDB

Include Sequences with Known StructuresDo Not use Structural Information Score 1Use Structural Information:Score 2

If Score1 ~ Score 2Structural Information does not help muchThe alignment is of reasonnable quality

Evaluating a Multiple Sequence AlignmentT-Coffee CORE indexFeature Based LibraryAPDB

Maninupulating and Comparing AlignmentsReformating/Processingseq_reformatextract_from_pdb

Coloringseq_reformatESCript

Comparingaln_compare

5

Thinking Large

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T-Coffee_dpaT-Coffee is limited to a small number of sequences

T-coffee_dpa: Double Progressive AlgoAble to handle large datasets1000 sequences and more

Able to use structural information

Using A Multiple Sequence Alignment

1

Exploring The Alignment

Exploring The Alignment

2

Using The Alignment

Does my Sequence Make Sense

Identifying Abnormalities within an MSA

Identifying Abnormalities within an MSA

Identifying Abnormalities within an MSA

Identifying Abnormalities within an MSAActivation loop (orange)

Identifying Abnormalities within an MSARetinoblastoma

2

Using The Alignment

Analysing the Structure withThe Alignment

The Evoltionnary Trace

3

Using The Alignment

Spotting differences

What makes a CDK not and AurorA

4

Clustering and Correlating

Function Trees Vs Lead Trees1-Select Functionnaly Important Positions2-Make a tree based on these positions3-Compare the tree with the lead tree

PROBLEMS:Choose on the right positionsDescribe the Leads with the right determinants