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TCOFFEE, a novel method for Multiple Sequence Alignments

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T-COFFEE, a novel method for Multiple Sequence Alignments. C dric Notredame ... Multiple Alignments Are CENTRAL to MOST Bioinformatics Techniques. ... – PowerPoint PPT presentation

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Title: TCOFFEE, a novel method for Multiple Sequence Alignments


1
T-COFFEE, a novel method for Multiple Sequence
Alignments
Cédric Notredame
2
Potential Uses of A Multiple Sequence Alignment?
chite ---ADKPKRPLSAYMLWLNSARESIKRENPDFK-VTEVAK
KGGELWRGLKD wheat --DPNKPKRAPSAFFVFMGEFREEFKQKNPK
NKSVAAVGKAAGERWKSLSE trybr KKDSNAPKRAMTSFMFFSSDFR
S----KHSDLS-IVEMSKAAGAAWKELGP mouse
-----KPKRPRSAYNIYVSESFQ----EAKDDS-AQGKLKLVNEAWKNLS
P . . .. . . .
. chite AATAKQNYIRALQEYERNGG- wheat
ANKLKGEYNKAIAAYNKGESA trybr AEKDKERYKREM---------
mouse AKDDRIRYDNEMKSWEEQMAE . .

Extrapolation
Phylogeny
Multiple Alignments Are CENTRAL to MOST
Bioinformatics Techniques.
Motifs/Patterns
Struc. Prediction
Profiles
3
Why Is It Difficult To Compute A multiple
Sequence Alignment?
A CROSSROAD PROBLEM
4
Why Is It Difficult To Compute A multiple
Sequence Alignment ?
BIOLOGY
COMPUTATION
CIRCULAR PROBLEM....
Good
Good
Alignment
Sequences
5
Progressive Alignment
6
The T-Coffee Algorithm
7
Progressive Alignment Principle and its
Limitations
8
The Extended Library Principle
9
The Extended Library Principle
10
The Triplet Assumption
SEQ A
SEQ B
11
Weighting And Extension
12
T-Coffee Progressive Alignment
Notredame, Higgins, Heringa, 2000
Dynamic Programming Using The extended Library
13
Mixing Local and Global Alignments
Global Alignment
Local Alignment
Extension
Multiple Sequence Alignment
14
What is a library?
2 Seq1 MySeq Seq2 MyotherSeq 1 2 1 1 25 3
8 70 .
3 Seq1 anotherseq Seq2 atsecondone Seq3
athirdone 1 2 1 1 25 1 3 3 8 70 .
ExtensionT-Coffee
Library Based Multiple Sequence Alignment
15
How Long Does it Take
16
(No Transcript)
17
N times slower than ClustalW
18
Validating T-Coffee
19
What Is BaliBase
BaliBase
BaliBase is a collection of reference Multiple
Alignments
The Structure of the Sequences are known and were
used to assemble the MALN.
Evaluation is carried out by Comparing the
Structure Based Reference Alignment With its
Sequence Based Counterpart
20
BaliBase
?
Method X
DALI, Sap
Comparison
21
Validation Using BaliBase
22
Validation Using BaliBase
23
Taking T-Coffee FurtherUsing Structures
24
Mixing Heterogenous Information With T-Coffee
Local Alignment
Global Alignment
Multiple Alignment
Structural
Specialist
Multiple Sequence Alignment
25
Running T-Coffee ONLINE
26
WHERE ?
Cedric.notredame_at_europe.com www.tcoffee.org
27
The T-Coffee Server
28
The T-Coffee Server
29
(No Transcript)
30
Future
31
Large Scale
32
Tailor Made
33
WHERE ?
Cedric.notredame_at_europe.com www.tcoffee.org
34
WHO ?
Orla OSullivan
35
(No Transcript)
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