Near-Optimal Block Alignments
The optimal alignment of two given biosequences is mathematically optimal, but it may not be a biologically optimal one. To investigate more possible alignments with biological meaning, one can relax the scoring functions to get near-optimal alignments. Though the near optimal alignments increase th...
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| Veröffentlicht in: | IEICE Transactions on Information and Systems 2008/03/01, Vol.E91.D(3), pp.789-795 |
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| container_title | IEICE Transactions on Information and Systems |
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| creator | TSENG, Kuo-Tsung YANG, Chang-Biau HUANG, Kuo-Si PENG, Yung-Hsing |
| description | The optimal alignment of two given biosequences is mathematically optimal, but it may not be a biologically optimal one. To investigate more possible alignments with biological meaning, one can relax the scoring functions to get near-optimal alignments. Though the near optimal alignments increase the possibility of finding the correct alignment, they may confuse the biologists because the size of candidates is large. In this paper, we present the filter scheme for the near-optimal alignments. An easy method for tracing the near-optimal alignments and an algorithm for filtering those alignments are proposed. The time complexity of our algorithm is O(dmn) in the worst case, where d is the maximum distance between the near-optimal alignments and the optimal alignment, and m and n are the lengths of the input sequences, respectively. |
| doi_str_mv | 10.1093/ietisy/e91-d.3.789 |
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Inf. & Syst.</addtitle><date>2008</date><risdate>2008</risdate><volume>E91.D</volume><issue>3</issue><spage>789</spage><epage>795</epage><pages>789-795</pages><issn>0916-8532</issn><issn>1745-1361</issn><eissn>1745-1361</eissn><abstract>The optimal alignment of two given biosequences is mathematically optimal, but it may not be a biologically optimal one. To investigate more possible alignments with biological meaning, one can relax the scoring functions to get near-optimal alignments. Though the near optimal alignments increase the possibility of finding the correct alignment, they may confuse the biologists because the size of candidates is large. In this paper, we present the filter scheme for the near-optimal alignments. An easy method for tracing the near-optimal alignments and an algorithm for filtering those alignments are proposed. 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| language | eng |
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| source | J-STAGE Free; EZB-FREE-00999 freely available EZB journals |
| subjects | Algorithms Alignment Applied sciences biosequence alignment Blocking computational biology Detection, estimation, filtering, equalization, prediction Exact sciences and technology Filtering Filtration Information, signal and communications theory longest common subsequence Mathematical analysis near-optimal alignments Optimization Scoring Signal and communications theory Signal, noise Telecommunications and information theory |
| title | Near-Optimal Block Alignments |
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