title: Constrained multiple sequence alignment tool development and its application to RNase family alignment.
abstract: 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.
authors.affiliation: Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, R.O.C. cytang@cs.nthu.edu.tw
authors.forename: Chuan Yi
authors.initials: CY
authors.lastname: Tang
authors.forename: Chin Lung
authors.initials: CL
authors.lastname: Lu
authors.forename: Margaret Dah-Tsyr
authors.initials: MD
authors.lastname: Chang
authors.forename: Yin-Te
authors.initials: YT
authors.lastname: Tsai
authors.forename: Yuh-Ju
authors.initials: YJ
authors.lastname: Sun
authors.forename: Kun-Mao
authors.initials: KM
authors.lastname: Chao
authors.forename: Jia-Ming
authors.initials: JM
authors.lastname: Chang
authors.forename: Yu-Han
authors.initials: YH
authors.lastname: Chiou
authors.forename: Chia-Mao
authors.initials: CM
authors.lastname: Wu
authors.forename: Hao-Teng
authors.initials: HT
authors.lastname: Chang
authors.forename: Wei-I
authors.initials: WI
authors.lastname: Chou
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D017124:Conserved Sequence; D008969:Molecular Sequence Data; D012260:Ribonucleases / Q000737:chemistry* / Q000145:classification; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D012260:Ribonucleases