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Aligning two RNA secondary structures with l-block

Paper ID Volume ID Publish Year Pages File Format Full-Text
14155 1177 2007 6 PDF Available
Aligning two RNA secondary structures with l-block

RNA sequences can form structures which are conserved throughout evolution and the question of aligning two RNA secondary structures has been extensively studied. Most of the previous alignment algorithms require the input of gap opening and gap extension penalty parameters. The choice of appropriate parameter values is controversial as there is little biological information to guide their assignment. In this paper, we present an algorithm which circumvents this problem. Instead of finding an optimal alignment with predefined gap opening penalty, the algorithm finds the optimal alignment with exact number of aligned blocks.

RNA secondary structure; Alignment; Aligned block
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Aligning two RNA secondary structures with l-block
Database: Elsevier - ScienceDirect
Journal: Biomolecular Engineering - Volume 24, Issue 3, September 2007, Pages 321–326
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Physical Sciences and Engineering Chemical Engineering Bioengineering