Recursive dynamic programming for adaptive sequence and structure alignment
- GMD SCAI, Sankt Augustin (Germany)
We propose a new alignment procedure that is capable of aligning protein sequences and structures in a unified manner. Recursive dynamic programming (RDP) is a hierarchical method which, on each level of the hierarchy, identifies locally optimal solutions and assembles them into partial alignments of sequences and/or structures. In contrast to classical dynamic programming, RDP can also handle alignment problems that use objective functions not obeying the principle of prefix optimality, e.g. scoring schemes derived from energy potentials of mean force. For such alignment problems, RDP aims at computing solutions that are near-optimal with respect to the involved cost function and biologically meaningful at the same time. Towards this goal, RDP maintains a dynamic balance between different factors governing alignment fitness such as evolutionary relationships and structural preferences. As in the RDP method gaps are not scored explicitly, the problematic assignment of gap cost parameters is circumvented. In order to evaluate the RDP approach we analyse whether known and accepted multiple alignments based on structural information can be reproduced with the RDP method.
- Research Organization:
- Stanford Univ., CA (United States)
- OSTI ID:
- 401868
- Report Number(s):
- CONF-9507246-; TRN: 96:005602-0046
- Resource Relation:
- Conference: Intelligent Systems for Molecular Biology (ISMB) conference, Cambridge (United Kingdom), 16-19 Jul 1995; Other Information: PBD: 1995; Related Information: Is Part Of ISMB-95 -- Third international conference on intelligent systems for molecular biology: Proceedings; Rawlings, C.; Clark, D.; Altman, R.; Hunter, L.; Lengauer, T.; Wodak, S. [eds.]; PB: 427 p.
- Country of Publication:
- United States
- Language:
- English
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