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PatternHunter: faster and more sensitive homology search

PatternHunter: faster and more sensitive homology search. Bin Ma, John Tromp and Ming Li Bioinformatics Vol. 18 no. 3 2002 Oxford University Press. Index. Introduction BLAST PatternHunter Comparison Conclusion References. Index. Introduction BLAST PatternHunter Comparison

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PatternHunter: faster and more sensitive homology search

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  1. PatternHunter: faster and more sensitive homology search Bin Ma, John Tromp and Ming Li Bioinformatics Vol. 18 no. 3 2002 Oxford University Press

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

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

  13. 1-hit performance comparison

  14. 2-hit performance comparison

  15. Performance comparison

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

  19. References • http://en.wikipedia.org/wiki/BLAST • http://bioinformatics.oxfordjournals.org/cgi/reprint/18/3/440.pdf • http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.1.2393&rep=rep1&type=pdf • http://books.google.es/books?hl=es&lr=&id=MRdpjtDbUcQC&oi=fnd&pg=PR11&dq=blast+oreilly&ots=1ROkssxuFf&sig=Lp2rNR5ZsOIeI7Bbt8PuZTuQp24

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