1. 6/2/20151 Bioinformatics & Parallel Computing Jessica Chiang

2. 6/2/20152 What is Bioinformatics? Also called biomedical computing. The application of computer science and technology to problems in the biomolecular sciences. Database & Internet (Algorithm..not specific to CS)

3. 6/2/20153 Mini intro to the bio terms DNA, RNA, protein Nucleotide sequence Protein folding

4. 6/2/20154 Sequence Similarity To determine the similarity between two DNA, RNA, or amino acid sequences String alignment problem S: acdbdb, T = cadbd a c - - b c d b - c ad b – d – C(S[i],T[j]) => scoring function

5. 6/2/20155 Alignment An alignment A maps S and T into strings S’ and T’ that may contain space characters (|S’| = |T’|) An optimal alignment of S and T is one that has the maximum possible alignment value To find the optimal alignment: most intuitive => O(2^(2*n)), n =|S| =|T|.

6. 6/2/20156 Using Dynamic Programming => O(n^2) First fill in the value of V(i,j) i \ j01,c2,a3,d4,b5,d 00-2-3-4-5 1,a 10 -2 2,c-2100-2 3,b-30021 4,c-4 11 5,d-5-2 103 6,b-6-3 032

7. 6/2/20157 Backtracing i \ j01,c2,a3,d4,b5,d 00< -1-2-3-4-5 1,a \ 10-2 2,c-2 10\ 0-2 3,b-3 00\ 21 4,c-4 ^ 11 5,d-5-2 10\ 3 6,b-6-3 0 3^ 2

8. 6/2/20158 Apps Based on Smith and Waterman Method FASTA, BLAST,FASTDB Use word-based or index-based searching, instead of full dynamic programming algorithm Why?

9. 6/2/20159 BLAZE Project of Dept of Biochemistry, Stanford Medical School (Brutlag) “An implementation of the Smith- Waterman Sequence Comparison Algorithm on a Massively Parallel Computer” 1993 paper

10. 6/2/201510 BLAZE continued Run on massively parallel MasPar MP1104 computer  4,096 4-bit processors with 256 MB of memory in total  Able to hold the entire database in memory at all times  Impressive result: improving sensitivity and maintaining interactivity(~22 million comparison per sec)

11. 6/2/201511 Related links http://www.ncbi.nlm.nih.gov/BLAST/ http://www.hgmp.mrc.ac.uk/Genome Web/docs-bioinformatics.html http://cmgm.stanford.edu/~brutlag/Pa pers/brutlag93.pdf http://www.cs.washington.edu/educat ion/courses/590bi/98w/