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Improved tools for biological sequence comparison

Improved tools for biological sequence comparison. Author : WILLIAM R. PEARSON, DAVID J. LIPMAN Publisher: Proc. Natl. Acad. Sci. USA 1988 Presenter: Hsin-Mao Chen Date: 2010/04/28. Outline. Introduction Step 1 Step 2 Step 3 Step 4 Result. Introduction. A heuristic method.

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Improved tools for biological sequence comparison

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  1. Improved tools for biological sequence comparison Author: WILLIAM R. PEARSON, DAVID J. LIPMAN Publisher: Proc. Natl. Acad. Sci. USA 1988 Presenter: Hsin-Mao Chen Date:2010/04/28

  2. Outline • Introduction • Step 1 • Step 2 • Step 3 • Step 4 • Result

  3. Introduction • A heuristic method. • The FASTA program is a more sensitive derivative of the FASTP program[1985].

  4. Introduction SW FASTA

  5. Step 1 • By using a lookup table to locate all identities between two DNA or amino acid sequences. • Dot matrix • Lookup table

  6. Step 1 Dot matrix

  7. Step 1 Lookup table 5 10 15 20 A: TCGGA TTCGT ACGGT ACGGA TC B: GTAAA CCACA ktup (k-tuple)=2

  8. Step 1 Lookup table 5 10 15 20 A: TCGGA TTCGTACGGT ACGGA TC B: GTAAA CCACA ktup (k-tuple)=2

  9. Step 1 Lookup table 5 10 15 20 A: TCGGA TTCGT ACGGTACGGA TC B: GTAAA CCACA ktup (k-tuple)=2

  10. Step 1

  11. Step 2 • Rescore these 10 regions using a scoring matrix (PAM250、Blosum50 ) and save the best initial regions greater than threshold.

  12. Step 2 PAM250

  13. Step 2

  14. Step 3 • FASTA calculates an optimal alignment of initial regions as a combination of compatible regions with maximal score.

  15. Step 3

  16. Step 4 • This final comparison considers all possible alignments of the query and library sequence that fall within a band centered around the highest scoring initial region.

  17. Step 4

  18. Result Ktup=4 IBM PCAT microcomputer Completed in under 15 min

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