Tang, Chuan YiChuan YiTangLu, Chin LungChin LungLuChang, Margaret Dah-TsyrMargaret Dah-TsyrChangTsai, Yin-TeYin-TeTsaiSun, Yuh-JuYuh-JuSunKUN-MAO CHAOChang, Jia-MingJia-MingChangChiou, Yu-HanYu-HanChiouWu, Chia-MaoChia-MaoWuChang, Hao-TengHao-TengChangChou, Wei-IWei-IChou2010-09-022018-07-052010-09-022018-07-052003-03http://ntur.lib.ntu.edu.tw//handle/246246/193607https://www.scopus.com/inward/record.uri?eid=2-s2.0-1842698155&doi=10.1142%2fS0219720003000095&partnerID=40&md5=95d0ee02949859c0d2adbc0d74fb2954In 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 alpha, then the time-complexity of our CMSA algorithm for aligning K sequences is O(alphaKn(4)), 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.en-USribonuclease; algorithm; amino acid sequence; article; chemistry; classification; comparative study; computer program; evaluation; methodology; molecular genetics; sequence alignment; sequence analysis; sequence homology; validation study; Algorithms; Amino Acid Sequence; Molecular Sequence Data; Ribonucleases; Sequence Alignment; Sequence Analysis, Protein; Sequence Homology, Amino Acid; Softwarejournal article10.1142/S0219720003000095152907732-s2.0-1842698155http://ntur.lib.ntu.edu.tw/bitstream/246246/193607/1/06.pdf