Patternhunter faster and more sensitive homology search
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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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