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 Institute for Algorithms and Scientific Computing SCAI

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

22 Scopus citations

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.

Original language	English
Title of host publication	Algorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings
Editors	Bernard M. E. Moret, Olivier Gascuel
Publisher	Springer
Pages	11-26
Number of pages	16
ISBN (Print)	3540425160
DOIs	https://doi.org/10.1007/3-540-44696-6_2
State	Published - 2001
Externally published	Yes
Event	1st International Workshop on Algorithms in Bioinformatics, WABI 2001 - Arhus, Denmark Duration: 28 Aug 2001 → 31 Aug 2001

Publication series

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

Conference

Conference	1st International Workshop on Algorithms in Bioinformatics, WABI 2001
Country/Territory	Denmark
City	Arhus
Period	28/08/01 → 31/08/01

Access to Document

10.1007/3-540-44696-6_2

Cite this

Von Öhsen, N., & Zimmer, R. (2001). Improving profile-profile alignments via log average scoring. In B. M. E. Moret, & O. Gascuel (Eds.), Algorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings (pp. 11-26). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 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. editor / Bernard M. E. Moret ; Olivier Gascuel. Springer, 2001. pp. 11-26 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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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 (eds), 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), vol. 2149, Springer, pp. 11-26, 1st International Workshop on Algorithms in Bioinformatics, WABI 2001, Arhus, Denmark, 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. ed. / Bernard M. E. Moret; Olivier Gascuel. Springer, 2001. p. 11-26 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2149).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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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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Von Öhsen N, Zimmer R. Improving profile-profile alignments via log average scoring. In Moret BME, Gascuel O, editors, Algorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings. Springer. 2001. p. 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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