A fragment based alignment in linear space
Sequence alignment is a very important problem in Bioinformatics since it is very useful to discover relationships among biological sequences. In this article we propose a new sequence alignment algorithm that is able to identify sequence similarities in linear space. Our solution is capable of usin...
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| creator | Correa, J. M. Melo, A. C. M. A. Jacobi, R. P. Boukerche, A. |
| description | Sequence alignment is a very important problem in Bioinformatics since it is very useful to discover relationships among biological sequences. In this article we propose a new sequence alignment algorithm that is able to identify sequence similarities in linear space. Our solution is capable of using several parameters specifying in which conditions a given residue can be aligned. This decision is taken based on a perceptron neuron and the best set of parameters is found using simulated annealing. Comparing our algorithm to a well established algorithm, we found that for pairwise alignments, our approach was faster for all instances tested with speedups up to 7.63 and yields better quality results for the majority of the instances. |
| doi_str_mv | 10.1109/BIBMW.2011.6112353 |
| format | Conference Proceeding |
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M.</creatorcontrib><creatorcontrib>Melo, A. C. M. A.</creatorcontrib><creatorcontrib>Jacobi, R. P.</creatorcontrib><creatorcontrib>Boukerche, A.</creatorcontrib><collection>IEEE Electronic Library (IEL) Conference Proceedings</collection><collection>IEEE Proceedings Order Plan All Online (POP All Online) 1998-present by volume</collection><collection>IEEE Xplore All Conference Proceedings</collection><collection>IEEE Electronic Library (IEL)</collection><collection>IEEE Proceedings Order Plans (POP All) 1998-Present</collection></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Correa, J. M.</au><au>Melo, A. C. M. A.</au><au>Jacobi, R. P.</au><au>Boukerche, A.</au><format>book</format><genre>proceeding</genre><ristype>CONF</ristype><atitle>A fragment based alignment in linear space</atitle><btitle>2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)</btitle><stitle>BIBMW</stitle><date>2011-11</date><risdate>2011</risdate><spage>42</spage><epage>49</epage><pages>42-49</pages><isbn>9781457716126</isbn><isbn>1457716127</isbn><eisbn>1457716135</eisbn><eisbn>9781457716133</eisbn><abstract>Sequence alignment is a very important problem in Bioinformatics since it is very useful to discover relationships among biological sequences. In this article we propose a new sequence alignment algorithm that is able to identify sequence similarities in linear space. Our solution is capable of using several parameters specifying in which conditions a given residue can be aligned. This decision is taken based on a perceptron neuron and the best set of parameters is found using simulated annealing. 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| subjects | Algorithm design and analysis Arrays Bioinformatics Dynamic programming Genomics Heuristic algorithms |
| title | A fragment based alignment in linear space |
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