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Bioinformatics & Parallel Computing

Bioinformatics & Parallel Computing. Jessica Chiang. 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). Mini intro to the bio terms.

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Bioinformatics & Parallel Computing

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  1. Bioinformatics & Parallel Computing Jessica Chiang

  2. 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. Mini intro to the bio terms • DNA, RNA, protein • Nucleotide sequence • Protein folding

  4. 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. 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. Using Dynamic Programming => O(n^2) • First fill in the value of V(i,j)

  7. Backtracing

  8. 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. 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. 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. Related links http://www.ncbi.nlm.nih.gov/BLAST/ http://www.hgmp.mrc.ac.uk/GenomeWeb/docs-bioinformatics.html http://cmgm.stanford.edu/~brutlag/Papers/brutlag93.pdf http://www.cs.washington.edu/education/courses/590bi/98w/

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