Smith–Waterman algorithm 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…

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. ——Mei…

生物信息原理作业第三弹:DNA序列局部比对,利用Smith–Waterman算法,python3.6代码实现. 实例以及原理均来自https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm. DNA序列局部比对 转载请保留出处! import numpy as np import pandas as pd sequence1 = 'TGTTACGG' sequence2 = 'GGTTGACTA' s1 = '' s2 = ''…

A recurrence plot (RP) is a straightforward way to visualize characteristics of similar system states attained at different times (Eckmann et al., 1987).  ,即RP可识别在时间上伸缩的状态对.Cross-Recurrent Plot,形成一个二维坐标轴,坐标系里的黑色代表相似的状态对,实际上在这个坐标系里,大部分的点都不是黑色的.在对角线上的路…

Multiple sequence alignment Benchmark Data set 1. 汇总: 序列比对标准数据集: http://www.drive5.com/bench/ This is a collection of multiple alignment benchmarks in a uniform format that is convenient for further analysis. All files are in FASTA format, with upper…

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The Baum-Welch algorithm is commonly used for training a Hidden Markov Model because of its superior numerical stability and its ability to guarantee the discovery of a locally maximum, Maximum Likelihood Estimator, in the presence of incomplete trai…

Machine Learning Methods: Decision trees and forests This post contains our crib notes on the basics of decision trees and forests. We first discuss the construction of individual trees, and then introduce random and boosted forests. We also discuss…

1352: New Sorting Algorithm Time Limit: 1 Sec  Memory Limit: 128 MB Description We are trying to use a new sorting algorithm to sort a sequence with distinct integers.    This algorithm will be end if the sequence is already in increasing order from…

让子弹飞一会 UVM框架,将验证平台和激励分开,env以下属于平台部分,test和sequence属于激励,这样各司其职.我们可以将sequence_item 比喻成子弹,sequencer 类比成弹夹,UVM平台就是个枪.如图所示uvm_sequence 的类继承关系. The sequence item is written by extending the uvm_sequence_item, uvm_sequence_item inherits from the uvm_object v…