{"title":"约束多序列比对工具的开发及其在RNase家族比对中的应用。","authors":"Chuan Yi Tang, Chin Lung Lu, Margaret Dah-Tsyr Chang, Yin-Te Tsai, Yuh-Ju Sun, Kun-Mao Chao, Jia-Ming Chang, Yu-Han Chiou, Chia-Mao Wu, Hao-Teng Chang, Wei-I Chou","doi":"","DOIUrl":null,"url":null,"abstract":"<p><p>In this paper, we design an 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 alpha, then the time-complexity of our CMSA algorithm for aligning K sequences is O (alphaKn4), where n is the maximum of the lengths of sequences. In addition, we have build 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.</p>","PeriodicalId":87204,"journal":{"name":"Proceedings. IEEE Computer Society Bioinformatics Conference","volume":"1 ","pages":"127-37"},"PeriodicalIF":0.0000,"publicationDate":"2002-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Constrained multiple sequence alignment tool development and its application to RNase family alignment.\",\"authors\":\"Chuan Yi Tang, Chin Lung Lu, Margaret Dah-Tsyr Chang, Yin-Te Tsai, Yuh-Ju Sun, Kun-Mao Chao, Jia-Ming Chang, Yu-Han Chiou, Chia-Mao Wu, Hao-Teng Chang, Wei-I Chou\",\"doi\":\"\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>In this paper, we design an 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 alpha, then the time-complexity of our CMSA algorithm for aligning K sequences is O (alphaKn4), where n is the maximum of the lengths of sequences. In addition, we have build 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.</p>\",\"PeriodicalId\":87204,\"journal\":{\"name\":\"Proceedings. IEEE Computer Society Bioinformatics Conference\",\"volume\":\"1 \",\"pages\":\"127-37\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2002-01-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Proceedings. IEEE Computer Society Bioinformatics Conference\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Proceedings. IEEE Computer Society Bioinformatics Conference","FirstCategoryId":"1085","ListUrlMain":"","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Constrained multiple sequence alignment tool development and its application to RNase family alignment.
In this paper, we design an 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 alpha, then the time-complexity of our CMSA algorithm for aligning K sequences is O (alphaKn4), where n is the maximum of the lengths of sequences. In addition, we have build 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.
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