A Block Recursive Algorithm for Sequence Alignment

Based on a new way to compute check points, this paper presents a "Block Recursive" sequence alignment algorithm, which can run in a time requirement between 1.5 mn and 3 mn in general cases but between 1.5 mn and 2 mn for sequences with high similarities. Still, the algorithm keeps a line...

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Published in:2008 2nd International Conference on Bioinformatics and Biomedical Engineering Vol. 2; pp. 604 - 607
Main Authors: Wang, Fang-Yuan, Li, Yu-Jian
Format: Conference Proceeding Journal Article
Language:English
Published: IEEE 2008
Subjects:
Computer science
Iterative algorithms
ISBN:9781424417476, 1424417473
ISSN:2151-7614
Online Access:Get full text
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Abstract Based on a new way to compute check points, this paper presents a "Block Recursive" sequence alignment algorithm, which can run in a time requirement between 1.5 mn and 3 mn in general cases but between 1.5 mn and 2 mn for sequences with high similarities. Still, the algorithm keeps a linear space requirement and always guarantees an optimal alignment result. Some experiments show that it runs at least 10% faster than the Hirschberg algorithm if the two compared sequences has a normalized edit distance less than 0.25.
AbstractList Based on a new way to compute check points, this paper presents a "Block Recursive" sequence alignment algorithm, which can run in a time requirement between 1.5 mn and 3 mn in general cases but between 1.5 mn and 2 mn for sequences with high similarities. Still, the algorithm keeps a linear space requirement and always guarantees an optimal alignment result. Some experiments show that it runs at least 10% faster than the Hirschberg algorithm if the two compared sequences has a normalized edit distance less than 0.25.
Based on a new way to compute check points, this paper presents a "Block Recursive" sequence alignment algorithm, which can run in a time requirement between 1.5 mn and 3 mn in general cases but between 1.5 mn and 2 mn for sequences with [abstract truncated by publisher].
Author Wang, Fang-Yuan
Li, Yu-Jian
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  organization: Coll. of Comput. Sci. & Technol., Beijing Univ. of Technol., Beijing
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Snippet Based on a new way to compute check points, this paper presents a "Block Recursive" sequence alignment algorithm, which can run in a time requirement between...
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SubjectTerms Computer science
Iterative algorithms
Title A Block Recursive Algorithm for Sequence Alignment
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