loading...
K-Group A* for Multiple Sequence Alignment with Quasi-Natural Gap Costs
Boca Raton, Florida November 15-November 17
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/ICTAI.2004.7716th IEEE International Conference on ...
 This Article 
 
PDF
HTML
 
 Share 
   
 Bibliographic References 
   
 Add to: 
 
Digg
Furl
Spurl
Blink
Simpy
Google
Del.icio.us
Y!MyWeb
 
 Search 
   
Rong Zhou, Mississippi State University
Eric A. Hansen, Mississippi State University
Alignment of multiple protein or DNA sequences is an important problem in Bioinformatics. Previous work has shown that the A* search algorithm can find optimal alignments for up to several sequences, and that a K-group generalization of A* can find approximate alignments for much larger numbers of sequences [6]. In this paper, we describe the first implementation of K-group A* that uses quasi-natural gap costs, the cost model used in practice by biologists. We also introduce a new method for computing gap-opening costs in profile alignment. Our results show that K-group A* can efficiently find optimal or close-to-optimal alignments for small groups of sequences, and, for large numbers of sequences, it can find higher-quality alignments than the widely-used CLUSTAL family of approximate alignment tools. This demonstrates the benefits of A* in aligning large numbers of sequences, as typically compared by biologists, and suggests that K-group A* could become a practical tool for multiple sequence alignment.
Citation:
Rong Zhou, Eric A. Hansen, "K-Group A* for Multiple Sequence Alignment with Quasi-Natural Gap Costs," ictai, pp.688-695, 16th IEEE International Conference on Tools with Artificial Intelligence (ICTAI'04), 2004
Usage of this product signifies your acceptance of the Terms of Use.