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 |
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| Main Authors: | , |
| Format: | Conference Proceeding Journal Article |
| Language: | English |
| Published: |
IEEE
2008
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| Subjects: | |
| ISBN: | 9781424417476, 1424417473 |
| ISSN: | 2151-7614 |
| Online Access: | Get full text |
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| Summary: | 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. |
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| Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| ISBN: | 9781424417476 1424417473 |
| ISSN: | 2151-7614 |
| DOI: | 10.1109/ICBBE.2008.147 |