Improving profile-profile alignments via log average scoring

Niklas Von Öhsen; Ralf Zimmer

doi:10.1007/3-540-44696-6_2

Improving profile-profile alignments via log average scoring

Niklas Von Öhsen
, Ralf Zimmer

Fraunhofer-Institut für Algorithmen und Wissenschaftliches Rechnen SCAI

Publikation: Beitrag in Buch/Bericht/Konferenzband › Konferenzbeitrag › Begutachtung

22 Zitate (Scopus)

Abstract

Alignments of frequency profiles against frequency profiles have a wide scope of applications in currently used bioinformatic analysis tools ranging from multiple alignment methods based on the progressive alignment approach to detecting of structural similarities based on remote sequence homology. We present the new log average scoring approach to calculating the score to be used with alignment algorithms like dynamic programming and show that it significantly outperforms the commonly used average scoring and dot product approach on a fold recognition benchmark. The score is also applicable to the problem of aligning two multiple alignments since every multiple alignment induces a frequency profile.

Originalsprache	Englisch
Titel	Algorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings
Redakteure/-innen	Bernard M. E. Moret, Olivier Gascuel
Herausgeber (Verlag)	Springer
Seiten	11-26
Seitenumfang	16
ISBN (Print)	3540425160
DOIs	https://doi.org/10.1007/3-540-44696-6_2
Publikationsstatus	Veröffentlicht - 2001
Extern publiziert	Ja
Veranstaltung	1st International Workshop on Algorithms in Bioinformatics, WABI 2001 - Arhus, Dänemark Dauer: 28 Aug. 2001 → 31 Aug. 2001

Publikationsreihe

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Band	2149
ISSN (Print)	0302-9743
ISSN (elektronisch)	1611-3349

Konferenz

Konferenz	1st International Workshop on Algorithms in Bioinformatics, WABI 2001
Land/Gebiet	Dänemark
Stadt	Arhus
Zeitraum	28/08/01 → 31/08/01

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10.1007/3-540-44696-6_2

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Von Öhsen, N., & Zimmer, R. (2001). Improving profile-profile alignments via log average scoring. in B. M. E. Moret, & O. Gascuel (Hrsg.), Algorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings (S. 11-26). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Band 2149). Springer. https://doi.org/10.1007/3-540-44696-6_2

Von Öhsen, Niklas ; Zimmer, Ralf. / Improving profile-profile alignments via log average scoring. Algorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings. Hrsg. / Bernard M. E. Moret ; Olivier Gascuel. Springer, 2001. S. 11-26 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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title = "Improving profile-profile alignments via log average scoring",

abstract = "Alignments of frequency profiles against frequency profiles have a wide scope of applications in currently used bioinformatic analysis tools ranging from multiple alignment methods based on the progressive alignment approach to detecting of structural similarities based on remote sequence homology. We present the new log average scoring approach to calculating the score to be used with alignment algorithms like dynamic programming and show that it significantly outperforms the commonly used average scoring and dot product approach on a fold recognition benchmark. The score is also applicable to the problem of aligning two multiple alignments since every multiple alignment induces a frequency profile.",

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Von Öhsen, N & Zimmer, R 2001, Improving profile-profile alignments via log average scoring. in BME Moret & O Gascuel (Hrsg.), Algorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Bd. 2149, Springer, S. 11-26, 1st International Workshop on Algorithms in Bioinformatics, WABI 2001, Arhus, Dänemark, 28/08/01. https://doi.org/10.1007/3-540-44696-6_2

Improving profile-profile alignments via log average scoring. / Von Öhsen, Niklas; Zimmer, Ralf.
Algorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings. Hrsg. / Bernard M. E. Moret; Olivier Gascuel. Springer, 2001. S. 11-26 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Band 2149).

Publikation: Beitrag in Buch/Bericht/Konferenzband › Konferenzbeitrag › Begutachtung

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AU - Zimmer, Ralf

N1 - Publisher Copyright: © Springer-Verlag Berlin Heidelberg 2001.

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Y1 - 2001

N2 - Alignments of frequency profiles against frequency profiles have a wide scope of applications in currently used bioinformatic analysis tools ranging from multiple alignment methods based on the progressive alignment approach to detecting of structural similarities based on remote sequence homology. We present the new log average scoring approach to calculating the score to be used with alignment algorithms like dynamic programming and show that it significantly outperforms the commonly used average scoring and dot product approach on a fold recognition benchmark. The score is also applicable to the problem of aligning two multiple alignments since every multiple alignment induces a frequency profile.

AB - Alignments of frequency profiles against frequency profiles have a wide scope of applications in currently used bioinformatic analysis tools ranging from multiple alignment methods based on the progressive alignment approach to detecting of structural similarities based on remote sequence homology. We present the new log average scoring approach to calculating the score to be used with alignment algorithms like dynamic programming and show that it significantly outperforms the commonly used average scoring and dot product approach on a fold recognition benchmark. The score is also applicable to the problem of aligning two multiple alignments since every multiple alignment induces a frequency profile.

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DO - 10.1007/3-540-44696-6_2

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AN - SCOPUS:84959053798

SN - 3540425160

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

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Von Öhsen N, Zimmer R. Improving profile-profile alignments via log average scoring. in Moret BME, Gascuel O, Hrsg., Algorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings. Springer. 2001. S. 11-26. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/3-540-44696-6_2

Improving profile-profile alignments via log average scoring

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