1. PatternHunter: faster and more sensitive homology search
Bin Ma, John Tromp and Ming Li
Bioinformatics Vol. 18 no
Oxford University Press

2. Index Introduction Comparison Conclusion References BLAST
PatternHunter
Comparison
Conclusion
References

3. Index Introduction Comparison Conclusion References BLAST
PatternHunter
Comparison
Conclusion
References

4. BLAST Basic Local Alignment Search Tool Steps: Seeding Extension
Evaluation

5. BLAST: Seeding PAM BLOSUM T > 10 PGQ (18) -> PAQ (12)
PGQ (18) -> PGA (11) …

6. BLAST: Extension 1-hit extension method 2-hit extension method
Cluster near and non-overlapped hits (< A).
Gapped Extension
Smith-Waterman algorithm variation.

7. BLAST: Evaluation

8. Index Introduction Comparison Conclusion References BLAST
PatternHunter
Comparison
Conclusion
References

9. PatternHunter
Steps
Seeding
Extension
¿Evaluation?

10. PatternHunter: Seeding
Optimal Spaced Seeds for Hidden Markov Models, with Application to Homologous Coding Regions. Brejová, B., Brown, D., Vinar T.

11. PatternHunter: Extension
1-hit extension method
If 1-hit fails
2-hit extension method
Cluster near and non-overlapped hits (< A).
Gapped Extension
Red-Black Tree algorithm variation.

12. Index Introduction Comparison Conclusion References BLAST
PatternHunter
Comparison
Conclusion
References

13. 1-hit performance comparison

14. 2-hit performance comparison

15. Performance comparison

16. Index Introduction Comparison Conclusion References BLAST
PatternHunter
Comparison
Conclusion
References

17. Conclusions
PatternHunter offers better results than BLAST, in terms of computation and search sensitivity.
Unlike BLAST, PatternHunter runs on all platforms that support Java.
BLAST algorithm, and its internal behavior, is widely known in bioinformatics.
Unlike PatternHunter, BLAST is licensed for public domain.
Homology search algorithms growing usage.

18. Index Introduction Comparison Conclusion References BLAST
PatternHunter
Comparison
Conclusion
References

19. References http://en.wikipedia.org/wiki/BLAST