PatternHunter: faster and more sensitive homology search

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Presentation transcript:

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 Comparison Conclusion References BLAST PatternHunter Comparison Conclusion References

Index Introduction Comparison Conclusion References BLAST PatternHunter Comparison Conclusion References

BLAST Basic Local Alignment Search Tool Steps: Seeding Extension Evaluation

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

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

BLAST: Evaluation

Index Introduction Comparison Conclusion References BLAST PatternHunter Comparison Conclusion References

PatternHunter Steps Seeding Extension ¿Evaluation?

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

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.

Index Introduction Comparison Conclusion References BLAST PatternHunter Comparison Conclusion References

1-hit performance comparison

2-hit performance comparison

Performance comparison

Index Introduction Comparison Conclusion References BLAST PatternHunter Comparison Conclusion References

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.

Index Introduction Comparison Conclusion References BLAST PatternHunter Comparison Conclusion References

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