DNA motif 搜索算法总结 2011-09-15 ~ ADMIN 翻译自:A survey of DNA motif finding algorithms, Modan K Das et. al., BMC Bioinformatics 2007, 8(suppl 7):S21 dio:10.1186/1471-2105-8-s7-s21 DNA功能域(motif)简单地讲就是一段特定模式的DNA序列,它之所以可以具有生物学功能是因为它的特殊序列可以和调控蛋白结合,比如转录因子,从而可以在…

[怪毛匠子]独家整理 不可以转载 MEME工具 http://meme-suite.org DNA motif 搜索算法总结 http://www.bbioo.com/lifesciences/40-115984-1.html online tools http://chipseek.cgu.edu.tw/main_menu.py RSAT http://rsat.sb-roscoff.fr https://bioconductor.org/help/course-materials/2010/…

DNA binding motif比对算法 2012-08-31 ~ ADMIN 之前介绍了序列比对的一些算法.本节主要讲述motif(有人翻译成结构模式,但本文一律使用基模)的比对算法. 那么什么是基模么?基模是对DNA结合位点的一种描述.它有几种描述方式,一种是共同序列(consensus sequences)一种是位点倾向距阵(Position Specific Frequency Matrices(PSFM))而对于PSFM,有两种表示方式,一种叫PCM,一种叫PFM,前者是Positi…

Problem Given two strings ss and tt, tt is a substring of ss if tt is contained as a contiguous collection of symbols in ss (as a result, tt must be no longer than ss). The position of a symbol in a string is the total number of symbols found to its…

Problem A common substring of a collection of strings is a substring of every member of the collection. We say that a common substring is a longest common substring if there does not exist a longer common substring. For example, "CG" is a common…

[SinGuLaRiTy-1039] Copyright (c) SinGuLaRiTy 2017. All Rights Reserved. 迭代加深搜索(ID) 迭代加深搜索,实质上就是限定下界的深度优先搜索.即首先允许深度优先搜索K层搜索树,若没有发现可行解,再将K+1后重复以上步骤搜索,直到搜索到可行解.在迭代加深搜索的算法中,连续的深度优先搜索被引入,每一个深度约束逐次加1,直到搜索到目标为止.迭代加深搜索算法就是仿广度优先搜索的深度优先搜索.既能满足深度优先搜索的线性存储要求,又能保…

All DNA is composed of a series of nucleotides abbreviated as A, C, G, and T, for example: "ACGAATTCCG". When studying DNA, it is sometimes useful to identify repeated sequences within the DNA. Write a function to find all the 10-letter-long seq…

来源:Kerson Huang, Lectures on Statistical Physics and Protein Folding, pp 24-25 把双链DNA解开就像拉拉链.设DNA有\(N\)个链环(link),每个链环有两种状态:闭合着或打开着,后一种状态比前一种状态的能量高\(\Delta\).打开的链环连续地排在一起,闭合的链环连续地排在一起,如下图所示.由于热涨落,链环会自发闭合或打开.问:打开的链环平均有多少? DNA的拉链模型 DNA的可能状态用打开的链环数目标记,\(…

题目链接 题意: 给n串有疾病的DNA序列,现有一串DNA序列,问最少修改几个DNA,能使新的DNA序列不含有疾病的DNA序列. 思路: 构建AC自动机,设定end结点,dp[i][j]表示长度i的前缀串走到自动机的j点最少需要修改几个DNA.状态转移方程.那么只要转移到下一个的DNA不是end结点就能转移,如果下一个DNA不和原序列不一样就+1. #include <bits/stdc++.h> const int N = 50 + 5; const int M = 1000 + 5; co…

All DNA is composed of a series of nucleotides abbreviated as A, C, G, and T, for example: "ACGAATTCCG". When studying DNA, it is sometimes useful to identify repeated sequences within the DNA. Write a function to find all the 10-letter-long seq…