1. BLAST a glimpse under the hood

2. Prospero: Our revels now are ended. These our actors, As I foretold you, were all spirits, and Are melted into air, into thin air: And like the baseless fabric of this vision, The cloud-capp'd tow'rs, the gorgeous palaces, The solemn temples, the great globe itself, Yea, all which it inherit, shall dissolve, And, like this insubstantial pageant faded, Leave not a rack behind. We are such stuff As dreams are made on; and our little life Is rounded with a sleep. find this

3. Prospero: Our revels now are ended. These our actors, As I foretold you, were all spirits, and Are melted into air, into thin air: And like the baseless fabric of this vision, The cloud-capp'd tow'rs, the gorgeous palaces, The solemn temples, the great globe itself, Yea, all which it inherit, shall dissolve, And, like this insubstantial pageant faded, Leave not a rack behind. We are such stuff As dreams are made on; and our little life Is rounded with a sleep. in here

4. Prospero: Our revels now are ended. These our actors, As I foretold you, were all spirits, and Are melted into air, into thin air: And like the baseless fabric of this vision, The cloud-capp'd tow'rs, the gorgeous palaces, The solemn temples, the great globe itself, Yea, all which it inherit, shall dissolve, And, like this insubstantial pageant faded, Leave not a rack behind. We are such stuff As dreams are made on; and our little life Is rounded with a sleep.

5. cloud-capp'd tow'rs cloud-capped towers cloudcapp'd towers cloud-tipped towels

6. cloud-capp'd tow'rs Our revels now are ended. These our actors, As I foretold you, were all spirits, and Are melted into air, into thin air: And like the baseless fabric of this vision, The cloud-capped towers, the gorgeous palaces, The solemn temples, the great globe itself, Yea, all which it inherit, shall dissolve, And, like this insubstantial pageant faded, cloud-capped towers

7. r: And like the baseless fabric of this vision, The cloud-capped towers, the gorgeous palaces, The solemn temples, the great globe itself, Yea, all which it inherit, shall dissolve, And, like this insubstantial pageant faded,

8. vision, The cloud-capped towers, the gorgeous palaces, The r: And like the baseless fabric of this vision, The cloud-capped towers, the gorgeous palaces, The + + + + + +

9. r: And like the baseless fabric of this vision, The cloud-capped towers, the gorgeous palaces, The solemn temples, the great globe itself, Yea, all which it inherit, shall dissolve, And, like this insubstantial pageant faded, vision, The cloud-capped towers, the gorgeous palaces, The + + + + + +

10. Natural scenario The

12. 1 Panda genome 1 gene in

13. ~ 2.30 gigabases (Gb) ~ 1 kilobase (kb) in

15. GenBank Panda genome

16. Describe the principle Describe the steps Discuss the concepts Use BLAST! Learning goals [BLAST]

17. Heuristic Ε ὑ ρίσκω

18. The algorithm in 13 steps

19. Information degree of surprise reduction in uncertainty

20. Prospero: Our revels now are ended. These our actors, As I foretold you, were all spirits, and Are melted into air, into thin air: And like the baseless fabric of this vision, The cloud-capp'd tow'rs, the gorgeous palaces, The solemn temples, the great globe itself, Yea, all which it inherit, shall dissolve, And, like this insubstantial pageant faded, Leave not a rack behind. We are such stuff As dreams are made on; and our little life Is rounded with a sleep.

22. 1. vifnknvikctgesqtgntgggqagntggdqagstggspqgstgaspqgst gaspqgstgasqpgssepsnpvssghsvstvsvsqtstssekqdtiqvks allkdymglkvtgpcnenfimflvphiyidvdtedtnielrttlkktnnaisfesn sgslekkkyvklpsngttgeqgsstgtvrgdtepisdsssssssssssssss sssssssssssseslpangpdsptvkpprnlqnicetgknfklvvyikent low complexity

23. 2. PAQILWQEDARRKGSM PAQ PAQI PAQIL PAQILW PAQILWQ PAQILWQE PAQILWQED… build word list nt words = 11 characters aa words = 3 characters

24. Biology BLAST 3. & 4. in

25. 3. evaluate matching words PAQ PAQI PAQIL PAQILW PAQILWQ PAQILWQE PAQILWQED… QVL QIA RIL … 8000 possible scores 20 x 20 x 20 e.g. score with BLOSUM

26. cloud-capp'd tow'rs cloud-capped towers cloudcapp'd towers cloud-tipped towels QVL QIA RIL … QIL

27. H K R E D N Q P IV L M F W Y S T C G A Hydrophobic Hydrophilic Aromatic Small Charged cyclic side-chain Amines Aliphatic - OH

28. retain high-scoring words QVL QIAQIA RIL … QIL 5 + 4 + 4 5 + 3 + 4 5 + 4 - 1 BLOSUM62 1 + 4 + 4 T = 10 8000 words  ca 50 4.

29. What about nucleotide words?

30. 5. Repeat 3. and 4. for each word listed A 50n polypeptide will yield ~12,500 words

31. 6. create search tree QIL QVL QII NIL Q QN QVQI QIIQIL V I LI QVL L N NI NIL I L

32. 7. plant seeds Query high-scoring words in position n Database n = 3  QIL, QVL … Exact matches

33. 8v18v1 grow HSPs + + + + + + stop when maximal score drops by a threshold X

34. vision, The cloud-capped towers, the gorgeous palaces, The r: And like the baseless fabric of this vision, The cloud-capped towers, the gorgeous palaces, The + + + + + +

35. The image of “cloud-capped towers”, unites ethereality and might vision, The cloud-capped towers, the gorgeous palaces, The - - - - - - - + - - - +

36. 8v28v2 grow HSPs use words at T  longer word list Query sequence Database sequence X X X X X X X A

37. 8v28v2 grow HSPs extend ‘close’ words as one X X A A

38. 9. filter HSPs HSP S cut-off score ≥ S ≤ S

39. 10. determine score significance Could 2 random sequences with the lengths of the query and database resp. score achieve the ≥ HSP score?

40. 10. determine score significance DB Query World of randomness S S* S** S*** S**** S***** S******

41. 10. determine score significance K, λ calculated for the scoring matrix m’ effective length of database seq n’ effective length of query seq

42. 10. determine score significance

43. 11. Extend ≥2 HSPs S 65405245 Poisson Sum of scores (65+40) > (52+45) 40 < 45

44. 12. Perform Smith-Waterman (local) alignments BLAST BLAST2 Calculate bit score (S’) and E-value of each SW alignment

45. 13. Deliver results E user selected cut-off score < E> E

46. BLAST A practical example

47. Mutation *

48. * * PCR Primer binding sites Transposon mutagenesis

49. * * PCR Seq 1Seq 2

50. BLAST Self-study