An Introduction to Multiple Sequence Alignments

1. An Introduction toMultiple Sequence Alignments Cédric Notredame

2. chite ---ADKPKRPLSAYMLWLNSARESIKRENPDFK-VTEVAKKGGELWRGLKD wheat --DPNKPKRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSE trybr KKDSNAPKRAMTSFMFFSSDFRS----KHSDLS-IVEMSKAAGAAWKELGP mouse -----KPKRPRSAYNIYVSESFQ----EAKDDS-AQGKLKLVNEAWKNLSP ***. ::: .: .. . : . . * . *: * chite AATAKQNYIRALQEYERNGG- wheat ANKLKGEYNKAIAAYNKGESA trybr AEKDKERYKREM--------- mouse AKDDRIRYDNEMKSWEEQMAE * : .* . :

3. Manguel M, Samaniego F.J., Abraham Wald’s Work on Aircraft Suvivability, J. American Statistical Association. 79, 259-270, (1984)

4. Our Scope How Can I Use My Alignment? How Does The Computer Align The Sequences? How Can I Assemble a Mult. Aln? What are the Difficulties?

5. Outline -Why Do We Need Multiple Sequence Alignment ? -The progressive Alignment Algorithm -A possible Strategy… -Potential Difficulties

6. Pre-requisite -How Do Sequences Evolve? -How can We COMPARE Sequences ? -How can We ALIGN Sequences ?

7. Why Do We Need Multiple Sequence Alignment ?

8. Sometimes Two Sequences Are Not Enough… The man with TWO watches NEVER knows the time

9. chite ---ADKPKRPLSAYMLWLNSARESIKRENPDFK-VTEVAKKGGELWRGLKD wheat --DPNKPKRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSE trybr KKDSNAPKRAMTSFMFFSSDFRS----KHSDLS-IVEMSKAAGAAWKELGP mouse -----KPKRPRSAYNIYVSESFQ----EAKDDS-AQGKLKLVNEAWKNLSP ***. ::: .: .. . : . . * . *: * chite AATAKQNYIRALQEYERNGG- wheat ANKLKGEYNKAIAAYNKGESA trybr AEKDKERYKREM--------- mouse AKDDRIRYDNEMKSWEEQMAE * : .* . : Structural Criteria: Evolution Criteria: Residues are arranged so that those playing a similar role end up in the same column. Residues are arranged so that those having the same ancestor end up in the same column. What is A Multiple Sequence Alignment?

10. PhylogenicRelation FunctionalRelation

12. chite ---ADKPKRPLSAYMLWLNSARESIKRENPDFK-VTEVAKKGGELWRGLKD wheat --DPNKPKRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSE trybr KKDSNAPKRAMTSFMFFSSDFRS----KHSDLS-IVEMSKAAGAAWKELGP unknown-----KPKRPRSAYNIYVSESFQ----EAKDDS-AQGKLKLVNEAWKNLSP ***. ::: .: .. . : . . * . *: * chite AATAKQNYIRALQEYERNGG- wheat ANKLKGEYNKAIAAYNKGESA trybr AEKDKERYKREM--------- unknown AKDDRIRYDNEMKSWEEQMAE * : .* . : Less Than 30 % id Extrapolation Beyond The Twilight Zone Homology? SwissProt Unkown Sequence How Can I Use A Multiple Sequence Alignment? BUT Conserved where it MATTERS

14. How Can I Use A Multiple Sequence Alignment? chite ---ADKPKRPLSAYMLWLNSARESIKRENPDFK-VTEVAKKGGELWRGLKD wheat --DPNKPKRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSE trybr KKDSNAPKRAMTSFMFFSSDFRS----KHSDLS-IVEMSKAAGAAWKELGP mouse -----KPKRPRSAYNIYVSESFQ----EAKDDS-AQGKLKLVNEAWKNLSP ***. ::: .: .. . : . . * . *: * chite AATAKQNYIRALQEYERNGG- wheat ANKLKGEYNKAIAAYNKGESA trybr AEKDKERYKREM--------- mouse AKDDRIRYDNEMKSWEEQMAE * : .* . : Extrapolation Prosite Patterns

15. How Can I Use A Multiple Sequence Alignment? chite ---ADKPKRPLSAYMLWLNSARESIKRENPDFK-VTEVAKKGGELWRGLKD wheat --DPNKPKRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSE trybr KKDSNAPKRAMTSFMFFSSDFRS----KHSDLS-IVEMSKAAGAAWKELGP mouse -----KPKRPRSAYNIYVSESFQ----EAKDDS-AQGKLKLVNEAWKNLSP ***. ::: .: .. . : . . * . *: * chite AATAKQNYIRALQEYERNGG- wheat ANKLKGEYNKAIAAYNKGESA trybr AEKDKERYKREM--------- mouse AKDDRIRYDNEMKSWEEQMAE * : .* . : Extrapolation P-K-R-[PA]-x(1)-[ST]… Prosite Patterns

16. How Can I Use A Multiple Sequence Alignment? chite ---ADKPKRPLSAYMLWLNSARESIKRENPDFK-VTEVAKKGGELWRGLKD wheat --DPNKPKRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSE trybr KKDSNAPKRAMTSFMFFSSDFRS----KHSDLS-IVEMSKAAGAAWKELGP mouse -----KPKRPRSAYNIYVSESFQ----EAKDDS-AQGKLKLVNEAWKNLSP ***. ::: .: .. . : . . * . *: * chite AATAKQNYIRALQEYERNGG- wheat ANKLKGEYNKAIAAYNKGESA trybr AEKDKERYKREM--------- mouse AKDDRIRYDNEMKSWEEQMAE * : .* . : Extrapolation Prosite Patterns SwissProt Uncharacterised Signature Match?

17. L? K>R A F D E F G H Q I V L W How Can I Use A Multiple Sequence Alignment? chite ---ADKPKRPLSAYMLWLNSARESIKRENPDFK-VTEVAKKGGELWRGLKD wheat --DPNKPKRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSE trybr KKDSNAPKRAMTSFMFFSSDFRS----KHSDLS-IVEMSKAAGAAWKELGP mouse -----KPKRPRSAYNIYVSESFQ----EAKDDS-IQGKLKLVNEAWKNLSP ***. ::: .: .. . : . . * . *: * chite AATAKQNYIRALQEYERNGG- wheat ANKLKGEYNKAIAAYNKGESA trybr AEKDKERYKREM--------- mouse AKDDRIRYDNEMKSWEEQMAE * : .* . : Extrapolation Prosite Patterns Profiles And HMMs -More Sensitive -More Specific

18. A Substitution Cost For Every Amino Acid, At Every Position A PROSITE PROFILE

19. How Can I Use A Multiple Sequence Alignment? chite ---ADKPKRPLSAYMLWLNSARESIKRENPDFK-VTEVAKKGGELWRGLKD wheat --DPNKPKRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSE trybr KKDSNAPKRAMTSFMFFSSDFRS----KHSDLS-IVEMSKAAGAAWKELGP mouse -----KPKRPRSAYNIYVSESFQ----EAKDDS-AQGKLKLVNEAWKNLSP ***. ::: .: .. . : . . * . *: * chite AATAKQNYIRALQEYERNGG- wheat ANKLKGEYNKAIAAYNKGESA trybr AEKDKERYKREM--------- mouse AKDDRIRYDNEMKSWEEQMAE * : .* . : Extrapolation chite wheat Motifs/Patterns trybr mouse Profiles -Evolution -Paralogy/Orthology Phylogeny

20. Column Constraint Evolution Constraint  Structure Constraint How Can I Use A Multiple Sequence Alignment? chite ---ADKPKRPLSAYMLWLNSARESIKRENPDFK-VTEVAKKGGELWRGLKD wheat --DPNKPKRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSE trybr KKDSNAPKRAMTSFMFFSSDFRS----KHSDLS-IVEMSKAAGAAWKELGP mouse -----KPKRPRSAYNIYVSESFQ----EAKDDS-AQGKLKLVNEAWKNLSP ***. ::: .: .. . : . . * . *: * chite AATAKQNYIRALQEYERNGG- wheat ANKLKGEYNKAIAAYNKGESA trybr AEKDKERYKREM--------- mouse AKDDRIRYDNEMKSWEEQMAE * : .* . : Extrapolation Motifs/Patterns Profiles Phylogeny Struc. Prediction

21. How Can I Use A Multiple Sequence Alignment? chite ---ADKPKRPLSAYMLWLNSARESIKRENPDFK-VTEVAKKGGELWRGLKD wheat --DPNKPKRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSE trybr KKDSNAPKRAMTSFMFFSSDFRS----KHSDLS-IVEMSKAAGAAWKELGP mouse -----KPKRPRSAYNIYVSESFQ----EAKDDS-AQGKLKLVNEAWKNLSP ***. ::: .: .. . : . . * . *: * chite AATAKQNYIRALQEYERNGG- wheat ANKLKGEYNKAIAAYNKGESA trybr AEKDKERYKREM--------- mouse AKDDRIRYDNEMKSWEEQMAE * : .* . : Extrapolation PsiPred OR PhD For secondary Structure Prediction: 75% Accurate. Motifs/Patterns Profiles Threading: is improving but is not yet as good. Phylogeny Struc. Prediction

22. Automatic Multiple Sequence Alignment methods are not always perfect… You know better… With your big BRAIN How Can I Use A Multiple Sequence Alignment? chite ---ADKPKRPLSAYMLWLNSARESIKRENPDFK-VTEVAKKGGELWRGLKD wheat --DPNKPKRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSE trybr KKDSNAPKRAMTSFMFFSSDFRS----KHSDLS-IVEMSKAAGAAWKELGP mouse -----KPKRPRSAYNIYVSESFQ----EAKDDS-AQGKLKLVNEAWKNLSP ***. ::: .: .. . : . . * . *: * chite AATAKQNYIRALQEYERNGG- wheat ANKLKGEYNKAIAAYNKGESA trybr AEKDKERYKREM--------- mouse AKDDRIRYDNEMKSWEEQMAE * : .* . :

24. BIOLOGY:What is A Good Alignment COMPUTATIONWhat is THE Good Alignment chite ---ADKPKRPLSAYMLWLNSARESIKRENPDFK-VTEVAKKGGELWRGLKD wheat --DPNKPKRAPSAFFVFMGEFREEFKQKNPKNKSVAAVGKAAGERWKSLSE trybr KKDSNAPKRAMTSFMFFSSDFRS----KHSDLS-IVEMSKAAGAAWKELGP mouse -----KPKRPRSAYNIYVSESFQ----EAKDDS-AQGKLKLVNEAWKNLSP ***. ::: .: .. . : . . * . *: * Why Is It Difficult To Compute A multiple Sequence Alignment? A CROSSROAD PROBLEM

25. Why Is It Difficult To Compute A multiple Sequence Alignment ? BIOLOGY COMPUTATION CIRCULAR PROBLEM.... Good Good Alignment Sequences

26. The Biological Problem. Same as PairWise Alignment Problem We do NOT know how Sequences Evolve. We do NOT understand the Relation Between Structures and Sequences. We would NOT recognize the Correct Alignment if we had it IN FRONT of our eyes…

27. The Biological Problem. The Charlie Chaplin Paradox

28. -A nice set of Sequences -Gap Penalties. AA A C C A C Sums of Pairs: Cost=6 A C A Over-estimation of the Substitutions Easy to compute The Biological Problem. How to Evaluate an Alignment -Substitution Matrix (Blosum) -An Evaluation Function

29. -A nice set of Sequences -Gap Penalties. GLOBAL Alignment Will It Work ? The COMPUTATIONAL Problem. Producing the Alignment -Substitution Matrix (Blosum) -An Evaluation Function -An Alignment Algorithm

30. HOW CAN I ALIGN MANYSEQUENCES 2 Globins =>1 Min

31. HOW CAN I ALIGN MANYSEQUENCES 3 Globins =>2 hours

32. HOW CAN I ALIGN MANYSEQUENCES 4 Globins => 10 days

33. HOW CAN I ALIGN MANYSEQUENCES 5 Globins => 3 years

34. HOW CAN I ALIGN MANYSEQUENCES !DHEALoaded 6 Globins =>300 years

35. HOW CAN I ALIGN MANYSEQUENCES 7 Globins =>30. 000 years Solidified Fossil,Old stuff

36. HOW CAN I ALIGN MANYSEQUENCES 8 Globins =>3 Million years

37. The Progressive Multiple Alignment Algorithm (Clustal W)

39. -Greedy Heuristic (No Guarranty). -Fast Making An Alignment Any Exact Method would be TOO SLOW We will use a Heuristic Algorithm. Progressive Alignment Algorithm is the most Popular -ClustalW

40. Progressive Alignment Feng and Dolittle, 1988; Taylor 1989 Clustering

41. Dynamic Programming Using A Substitution Matrix Progressive Alignment

42. Progressive Alignment -Depends on the CHOICE of the sequences. -Depends on the ORDER of the sequences (Tree). • -Depends on the PARAMETERS: • Substitution Matrix. • Penalties (Gop, Gep). • Sequence Weight. • Tree making Algorithm.

43. Progressive Alignment When Does It Work Works Well When Phylogeny is Dense No outlayer Sequence. Image: River Crossing

44. CLUSTALW (Score=20, Gop=-1, Gep=0, M=1) SeqA GARFIELD THE LAST FA-T CAT SeqB GARFIELD THE FAST CA-T --- SeqC GARFIELD THE VERY FAST CAT SeqD -------- THE ---- FA-T CAT CORRECT (Score=24) SeqA GARFIELD THE LAST FA-T CAT SeqB GARFIELD THE FAST ---- CAT SeqC GARFIELD THE VERY FAST CAT SeqD -------- THE ---- FA-T CAT Progressive Alignment When Doesn’t It Work

45. GARFIELD THE LAST FAT CAT GARFIELD THE LAST FAT CAT GARFIELD THE FAST CAT --- GARFIELD THE FAST CAT GARFIELD THE LAST FA-T CAT GARFIELD THE FAST CA-T --- GARFIELD THE VERY FAST CAT -------- THE ---- FA-T CAT GARFIELD THE VERY FAST CAT GARFIELD THE VERY FAST CAT -------- THE ---- FA-TCAT THE FAT CAT

46. Building the Right Multiple Sequence Alignment.

47. Recognizing The Right Sequences When you Meet Them…

48. Gathering Sequences: BLAST

49. Common Mistake: Sequences Too Closely Related PRVA_MACFU SMTDLLNAEDIKKAVGAFSAIDSFDHKKFFQMVGLKKKSADDVKKVFHILDKDKSGFIEE PRVA_HUMAN SMTDLLNAEDIKKAVGAFSATDSFDHKKFFQMVGLKKKSADDVKKVFHMLDKDKSGFIEE PRVA_GERSP SMTDLLSAEDIKKAIGAFAAADSFDHKKFFQMVGLKKKTPDDVKKVFHILDKDKSGFIEE PRVA_MOUSE SMTDVLSAEDIKKAIGAFAAADSFDHKKFFQMVGLKKKNPDEVKKVFHILDKDKSGFIEE PRVA_RAT SMTDLLSAEDIKKAIGAFTAADSFDHKKFFQMVGLKKKSADDVKKVFHILDKDKSGFIEE PRVA_RABIT AMTELLNAEDIKKAIGAFAAAESFDHKKFFQMVGLKKKSTEDVKKVFHILDKDKSGFIEE :**::*.*******:***:* :****************..::******:*********** PRVA_MACFU DELGFILKGFSPDARDLSAKETKTLMAAGDKDGDGKIGVDEFSTLVAES PRVA_HUMAN DELGFILKGFSPDARDLSAKETKMLMAAGDKDGDGKIGVDEFSTLVAES PRVA_GERSP DELGFILKGFSSDARDLSAKETKTLLAAGDKDGDGKIGVEEFSTLVSES PRVA_MOUSE DELGSILKGFSSDARDLSAKETKTLLAAGDKDGDGKIGVEEFSTLVAES PRVA_RAT DELGSILKGFSSDARDLSAKETKTLMAAGDKDGDGKIGVEEFSTLVAES PRVA_RABIT EELGFILKGFSPDARDLSVKETKTLMAAGDKDGDGKIGADEFSTLVSES :*** ******.******.**** *:************.:******:** -IDENTICAL SEQUENCES BRING NO INFORMATION FOR THE MULTIPLE SEQUENCE ALIGNMENT -MULTIPLE SEQUENCE ALIGNMENTS THRIVE ON DIVERSITY…