(2013). A Knowledge-Based Multiple-Sequence Alignment Algorithm. IEEE/ACM Trans Comput Biol Bioinform., 10(4), 884-896.D. N. Ken and Y. Pan, "A knowledge-based multiple-sequence alignment algorithm," IEEE/ACM Trans. Comput. Biol. Bioinf., vol. 10, no. 4, pp. 884-896, Jul./Aug...
Ref:Lassmann T, Sonnhammer E L L. Kalign–an accurate and fast multiple sequence alignment algorithm[J]. BMC bioinformatics, 2005, 6(1): 298. FFT变换 蛋白质字母比较的时候要查表,比较麻烦。有人用一个二维向量代替每一个字母,字母比较变成了二维向量之间的距离;kmer(就是k-gram)之间的比较转换成向...
首先需要澄清一个事实,Smith–Waterman algorithm是求两个序列的最佳subsequence匹配,与之对应的算法但是求两个序列整体匹配的算法是Needleman-Wusch algorithm,即 Smith–Waterman algorithm:Local Needleman-Wusch algorithm: Global Needleman-Wusch algorithm与longest common subsequence (LCS)很相似,最大差别在于它给LCS...
In this article we propose a Fast Optimal Global Sequence Alignment Algorithm, FOGSAA, which aligns a pair of nucleotide/protein sequences faster than any optimal global alignment method including the widely used Needleman-Wunsch (NW) algorithm. FOGSAA is applicable for all types of sequences, wi...
本系列介绍几种序列对齐方法,包括Dynamic time warping (DTW),Smith–Waterman algorithm,Cross-recurrence plot Dynamic time warping (DTW) is a well-known technique to find an optimal alignment between two given (time-dependent) sequences under certain restrictions. ...
ResearchofBiologicalSequenceAlignmentAlgorithmand GraphicsHardwareAcceleration ZHANGLinCHAIHuiWOLi-Ke WOXing-De 10.3969/j.issn.0258..8021.2011.06.009 2011-03-022011-08-2 国家自然科学基金(30873366);浙江省医药卫生科学研究基金(2009B112);浙江省教育厅资助项目(Y200906336) 30卷 6期 @@[1] 张阳德.生物信息...
BMC Bioinformatics 2010, 11:235 http://www.biomedcentral.com/1471-2105/11/235 SOFTWARE Open Access MTRAP: Pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues Toshihide Hara*, Keiko Sato, Masanori Ohya Abstract Background:...
multiple alignment Detail algorithm for center star method Step 1 Step 2 Step 3 Step 4 Step 1 O(k 2 n 2 ) Step 2 O(k 2 ) Step 3 O(kn 2 ) Step 4 O(k 2 n) Running time of center star method Assume all k sequences are of length n. Step 1 takes O(k 2 n 2 ) time...
By our experiments, both the alignment quality and required time of our algorithm are better than Clustal W algorithm (using the neighboring joining method).doi:10.1093/bioinformatics/bth468Kuen-feng H...
6. Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost [O] . Shinsuke Yamada, Osamu Gotoh, Hayato Yamana 2006 机译:使用具有分段线性缺口成本的新型组间序列比对算法提高多序列比对的准确性 7. Improvement in ...