Alignments
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Allignment slides for bioinf4biologists course 2009
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Alignments
- 1. Multiple Sequence Alignment James McInerney bioinf4biologists Feb. 2009
- 2. Alignment can be easy or difficult Easy Difficult due to insertions or deletions (indels)
- 9. Alignment of 16S rRNA can be guided by secondary structure Alignment of 16S rRNA sequences from different bacteria
- 10. Protein Alignment may be guided by Tertiary Structure Interactions Homo sapiens DjlA protein Escherichia coli DjlA protein
- 13. Local minimum GARFIELDTHEFAT---CAT GARFIELDTHEFATFATCAT
- 20. Example dotplot - repeated domains in Drosophila melanogaster SLIT protein Swiss-prot entry For further discussion of dotplot see Attwood and Parry-Smith p116-8
- 23. Overview of ClustalW Procedure 1 PEEKSAVTALWGKVN--VDEVGG 2 GEEKAAVLALWDKVN--EEEVGG 3 PADKTNVKAAWGKVGAHAGEYGA 4 AADKTNVKAAWSKVGGHAGEYGA 5 EHEWQLVLHVWAKVEADVAGHGQ Hbb_Human 1 - Hbb_Horse 2 .17 - Hba_Human 3 .59 .60 - Hba_Horse 4 .59 .59 .13 - Myg_Whale 5 .77 .77 .75 .75 - Hbb_Human Hbb_Horse Hba_Horse Hba_Human Myg_Whale 2 1 3 4 2 1 3 4 alpha-helices Quick pairwise alignment: calculate distance matrix Neighbor-joining tree (guide tree) Progressive alignment following guide tree CLUSTAL W
- 25. Path Graph for aligning two sequences.
- 27. Alignment using this path GATTC- GAATTC 1 1 0 1 0 -1
- 28. Optimal Alignment 1 1 1 -1 1 1 1 Alignment score: 4 Alignment using this path GA-TTC GAATTC
- 29. Optimal Alignment 2 1 -1 1 1 1 1 Alignment score: 4 Alignment using this path G-ATTC GAATTC
- 30. Alignment of 3 sequences
- 33. Distance Matrix What is required for the Neighbour joining method? Distance matrix
- 34. First Step PAM distance 3.3 (Human - Monkey) is the minimum. So we'll join Human and Monkey to MonHum and we'll calculate the new distances. Mon-Hum Monkey Human Spinach Mosquito Rice
- 35. Calculation of New Distances After we have joined two species in a subtree we have to compute the distances from every other node to the new subtree. We do this with a simple average of distances: Dist[Spinach, MonHum] = (Dist[Spinach, Monkey] + Dist[Spinach, Human])/2 = (90.8 + 86.3)/2 = 88.55 Mon-Hum Monkey Human Spinach
- 36. Next Cycle Human Mosquito Mon-Hum Monkey Spinach Rice Mos-(Mon-Hum)
- 37. Penultimate Cycle Human Mosquito Mon-Hum Monkey Spinach Rice Mos-(Mon-Hum) Spin-Rice
- 38. Last Joining Human Mosquito Mon-Hum Monkey Spinach Rice Mos-(Mon-Hum) Spin-Rice (Spin-Rice)-(Mos-(Mon-Hum))
- 39. Unrooted Neighbor-Joining Tree Human Monkey Mosquito Rice Spinach
- 44. Progressive alignment - step 1 1. gctcgatacgatacgatgactagcta 2. gctcgatacaagacgatgacagcta 3. gctcgatacacgatgactagcta 4. gctcgatacacgatgacgagcga 5. ctcgaacgatacgatgactagct 1. gctcgatacgatacgatgactagcta 2. gctcgatacaagacgatgac-agcta 1 2 3 4 5
- 45. Progressive alignment - step 2 1. gctcgatacgatacgatgactagcta 2. gctcgatacaagacgatgacagcta 3. gctcgatacacgatgactagcta 4. gctcgatacacgatgacgagcga 5. ctcgaacgatacgatgactagct 3. gctcgatacacgatgactagcta 4. gctcgatacacgatgacgagcga 1 2 3 4 5
- 46. Progressive alignment - step 3 1. gctcgatacgatacgatgactagcta 2. gctcgatacaagacgatgac-agcta + 3. gctcgatacacgatgactagcta 4. gctcgatacacgatgacgagcga 1. gctcgatacgatacgatgactagcta 2. gctcgatacaagacgatgac-agcta 3. gctcgatacacga---tgactagcta 4. gctcgatacacga---tgacgagcga 1 2 3 4 5
- 47. Progressive alignment - final step 1. gctcgatacgatacgatgactagcta 2. gctcgatacaagacgatgac-agcta 3. gctcgatacacga---tgactagcta 4. gctcgatacacga---tgacgagcga + 5. ctcgaacgatacgatgactagct 1. gctcgatacgatacgatgactagcta 2. gctcgatacaagacgatgac-agcta 3. gctcgatacacga---tgactagcta 4. gctcgatacacga---tgacgagcga 5. -ctcga-acgatacgatgactagct- 1 2 3 4 5