{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T20:26:55Z","timestamp":1761596815997},"reference-count":33,"publisher":"World Scientific Pub Co Pte Lt","issue":"02","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2003,7]]},"abstract":"<jats:p> In this paper, we design a heuristic algorithm of computing a constrained multiple sequence alignment (CMSA for short) for guaranteeing that the generated alignment satisfies the user-specified constraints that some particular residues should be aligned together. If the number of residues needed to be aligned together is a constant \u03b1, then the time-complexity of our CMSA algorithm for aligning K sequences is O(\u03b1Kn<jats:sup>4<\/jats:sup>), where n is the maximum of the lengths of sequences. In addition, we have built up such a CMSA software system and made several experiments on the RNase sequences, which mainly function in catalyzing the degradation of RNA molecules. The resulting alignments illustrate the practicability of our method. <\/jats:p>","DOI":"10.1142\/s0219720003000095","type":"journal-article","created":{"date-parts":[[2003,7,21]],"date-time":"2003-07-21T10:06:17Z","timestamp":1058781977000},"page":"267-287","source":"Crossref","is-referenced-by-count":36,"title":["Constrained Multiple Sequence Alignment Tool Development and Its Application to RNase Family Alignment"],"prefix":"10.1142","volume":"01","author":[{"given":"Chuan Yi","family":"Tang","sequence":"first","affiliation":[{"name":"Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC"}]},{"given":"Chin Lung","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Biological Science  and Technology, National Chiao Tung University, Hsinchu 300, Taiwan, ROC"}]},{"given":"Margaret Dah-Tsyr","family":"Chang","sequence":"additional","affiliation":[{"name":"Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC"}]},{"given":"Yin-Te","family":"Tsai","sequence":"additional","affiliation":[{"name":"Department of Computer Science and  Information Management, Providence University, Shalu, Taichung Hsien 433,  Taiwan, ROC"}]},{"given":"Yuh-Ju","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC"}]},{"given":"Kun-Mao","family":"Chao","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan, ROC"}]},{"given":"Jia-Ming","family":"Chang","sequence":"additional","affiliation":[{"name":"Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC"}]},{"given":"Yu-Han","family":"Chiou","sequence":"additional","affiliation":[{"name":"Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC"}]},{"given":"Chia-Mao","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC"}]},{"given":"Hao-Teng","family":"Chang","sequence":"additional","affiliation":[{"name":"Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC"}]},{"given":"Wei-I","family":"Chou","sequence":"additional","affiliation":[{"name":"Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC"}]}],"member":"219","published-online":{"date-parts":[[2012,1,25]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1137\/0149012"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1016\/S0304-3975(97)00023-6"},{"key":"rf3","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(02)01036-7"},{"key":"rf4","doi-asserted-by":"publisher","DOI":"10.1016\/S0304-3975(99)00324-2"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1137\/0148063"},{"key":"rf6","doi-asserted-by":"publisher","DOI":"10.1007\/BF02459635"},{"key":"rf7","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/16.22.10881"},{"key":"rf8","volume-title":"Pattern Classification and Scene Analysis","author":"Duda R. 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