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Enhancing Bioinformatics Searches with PatternHunter Algorithm

The PatternHunter algorithm provides a faster and more sensitive homology search compared to BLAST. This study by Bin Ma, John Tromp, and Ming Li in 2002 discusses the steps involved in PatternHunter, including seeding, extension, and evaluation, highlighting its benefits over traditional approaches. Unlike BLAST, PatternHunter runs on Java-supported platforms, offering better computation and search sensitivity. The algorithm's performance is compared with BLAST, showcasing its superiority. Homology search algorithms are gaining popularity in bioinformatics, with PatternHunter showing promising results.

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Enhancing Bioinformatics Searches with PatternHunter Algorithm

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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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