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...
Loving, A bit parallel, general integer-scoring sequence alignment algorithm, Proc. 24th Symposium on Combinatorial Pattern Matching (CPM), 2013, pp. 50-61.Gary Benson, Yozen Hernandez, and Joshua Loving. A Bit-Parallel, General Integer-Scoring Sequence Alignment Algorithm, pages 50-61. Springer...
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. ——Meinard Muller的《Information Retriev...
(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...
Needleman-Wusch algorithm与longest common subsequence (LCS)很相似,最大差别在于它给LCS中增、减、替换等操作赋予了不同的负权值,甚至不同的匹配对(a,a),(b,b)也有不同的正权值。可以这么说,Needleman-Wusch algorithm是改进的LCS算法。主要解决如下谁最优的问题: ...
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...
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...
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...
BitPAl: a bit-parallel, general integer-scoring sequence alignment algorithm. Loving J, Hernandez Y, Benson G. BitPAl: a bit-parallel, general integer-scoring sequence alignment algorithm. Bioinformatics. 2014;30(22):3166-73... Loving,Joshua,Hernandez,... - 《Bioinformatics》 被引量: 11发表...
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:...