Estimating seed sensitivity on homogeneous alignments

Gregory Kucherov; Laurent Noé; Yann Ponty

doi:10.1109/BIBE.2004.1317369

Estimating seed sensitivity on homogeneous alignments

Gregory Kucherov
, Laurent Noé
, Yann Ponty

LORIA Laboratoire Lorrain de Recherche en Informatique et ses Applications
INRIA Saclay, Laboratoire de Recherche en Informatique (LRI), Université Paris Sud

Résultats de recherche: Le chapitre dans un livre, un rapport, une anthologie ou une collection › Contribution à une conférence › Revue par des pairs

Résumé

We address the problem of estimating the sensitivity of seed-based similarity search algorithms. In contrast to approaches based on Markov models [18, 6, 3, 4, 10], we study the estimation based on homogeneous alignments. We describe an algorithm for counting and random generation of those alignments and an algorithm for exact computation of the sensitivity for a broad class of seed strategies. We provide experimental results demonstrating a bias introduced by ignoring the homogeneousness condition.

langue originale	Anglais
titre	Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004
Editeur	IEEE Computer Society
Pages	387-394
Nombre de pages	8
ISBN (imprimé)	0769521738, 9780769521732
Les DOIs	https://doi.org/10.1109/BIBE.2004.1317369
état	Publié - 1 janv. 2004
Modification externe	Oui
Evénement	Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 - Taichung, Taiwan Durée: 19 mai 2004 → 21 mai 2004

Série de publications

Nom	Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004

Une conférence

Une conférence	Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004
Pays/Territoire	Taiwan
La ville	Taichung
période	19/05/04 → 21/05/04

Accès au document

10.1109/BIBE.2004.1317369

Contient cette citation

@inproceedings{ffe69dfc06384411954ec91a73abdf09,

title = "Estimating seed sensitivity on homogeneous alignments",

abstract = "We address the problem of estimating the sensitivity of seed-based similarity search algorithms. In contrast to approaches based on Markov models [18, 6, 3, 4, 10], we study the estimation based on homogeneous alignments. We describe an algorithm for counting and random generation of those alignments and an algorithm for exact computation of the sensitivity for a broad class of seed strategies. We provide experimental results demonstrating a bias introduced by ignoring the homogeneousness condition.",

author = "Gregory Kucherov and Laurent No{\'e} and Yann Ponty",

year = "2004",

month = jan,

day = "1",

doi = "10.1109/BIBE.2004.1317369",

language = "English",

isbn = "0769521738",

series = "Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004",

publisher = "IEEE Computer Society",

pages = "387--394",

booktitle = "Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004",

note = "Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004 ; Conference date: 19-05-2004 Through 21-05-2004",

}

Kucherov, G, Noé, L & Ponty, Y 2004, Estimating seed sensitivity on homogeneous alignments. Dans Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004. Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004, IEEE Computer Society, p. 387-394, Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004, Taichung, Taiwan, 19/05/04. https://doi.org/10.1109/BIBE.2004.1317369

Estimating seed sensitivity on homogeneous alignments. / Kucherov, Gregory; Noé, Laurent; Ponty, Yann.
Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004. IEEE Computer Society, 2004. p. 387-394 (Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004).

Résultats de recherche: Le chapitre dans un livre, un rapport, une anthologie ou une collection › Contribution à une conférence › Revue par des pairs

TY - GEN

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N2 - We address the problem of estimating the sensitivity of seed-based similarity search algorithms. In contrast to approaches based on Markov models [18, 6, 3, 4, 10], we study the estimation based on homogeneous alignments. We describe an algorithm for counting and random generation of those alignments and an algorithm for exact computation of the sensitivity for a broad class of seed strategies. We provide experimental results demonstrating a bias introduced by ignoring the homogeneousness condition.

AB - We address the problem of estimating the sensitivity of seed-based similarity search algorithms. In contrast to approaches based on Markov models [18, 6, 3, 4, 10], we study the estimation based on homogeneous alignments. We describe an algorithm for counting and random generation of those alignments and an algorithm for exact computation of the sensitivity for a broad class of seed strategies. We provide experimental results demonstrating a bias introduced by ignoring the homogeneousness condition.

U2 - 10.1109/BIBE.2004.1317369

DO - 10.1109/BIBE.2004.1317369

M3 - Conference contribution

AN - SCOPUS:4544227949

SN - 0769521738

SN - 9780769521732

T3 - Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004

SP - 387

EP - 394

BT - Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004

PB - IEEE Computer Society

T2 - Proceedings - Fourth IEEE Symposium on Bioinformatics and Bioengineering, BIBE 2004

Y2 - 19 May 2004 through 21 May 2004

ER -

Estimating seed sensitivity on homogeneous alignments

Résumé

Série de publications

Une conférence

Accès au document

Empreinte digitale

Contient cette citation