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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

PatternHunter: faster and more sensitive homology search

Bin Ma, John Tromp and Ming Li

Bioinformatics Vol. 18 no. 3 2002

Oxford University Press

index
Index
  • Introduction
    • BLAST
    • PatternHunter
  • Comparison
  • Conclusion
  • References
index1
Index
  • Introduction
    • BLAST
    • PatternHunter
  • Comparison
  • Conclusion
  • References
blast
BLAST
  • Basic Local Alignment Search Tool
  • Steps:
    • Seeding
    • Extension
    • Evaluation
blast seeding
BLAST: Seeding

PAM BLOSUM

T > 10

PGQ (18) -> PAQ (12)

PGQ (18) -> PGA (11)

blast extension
BLAST: Extension

1-hit extension method

2-hit extension method

Cluster near and non-overlapped hits (< A).

Gapped Extension

Smith-Waterman algorithm variation.

index2
Index
  • Introduction
    • BLAST
    • PatternHunter
  • Comparison
  • Conclusion
  • References
patternhunter
PatternHunter
  • Steps
    • Seeding
    • Extension
    • ¿Evaluation?
patternhunter seeding
PatternHunter: Seeding

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

patternhunter extension
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.

index3
Index
  • Introduction
    • BLAST
    • PatternHunter
  • Comparison
  • Conclusion
  • References
index4
Index
  • Introduction
    • BLAST
    • PatternHunter
  • Comparison
  • Conclusion
  • References
conclusions
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.
index5
Index
  • Introduction
    • BLAST
    • PatternHunter
  • Comparison
  • Conclusion
  • References
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
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