Rosalind Java
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Rosalind Java|Speeding Up Motif Finding
Rosalind编程问题之计算错误矩阵(failure array)输出前后缀检索匹配。原创 2024-01-12 19:05:11 · 516 阅读 · 0 评论 -
Rosalind Java|Matching Random Motifs
Rosalind编程问题之计算随机序列出现并匹配待比对序列的概率。跟有异曲同工之妙。原创 2022-10-05 22:52:37 · 513 阅读 · 0 评论 -
Rosalind Java|Introduction to Set Operations
Rosalind编程问题之集合操作。题不难,但是格式处理繁琐。原创 2022-07-25 15:40:53 · 218 阅读 · 0 评论 -
Rosalind Java|Introduction to Random Strings
Rosalind编程问题之计算随机序列出现概率的公共对数。这道题让小编想起了被GRE支配的恐惧,能看懂你就会做。原创 2022-07-14 14:07:17 · 182 阅读 · 0 评论 -
Rosalind Java|Genome Assembly as Shortest Superstring
Rosalind编程问题之基因组reads组装。终于来到基因组装部分了~这里分享最简单的组装逻辑之一,即根据重叠序列左右延伸出最长序列。Problem:For a collection of strings, a larger string containing every one of the smaller strings as a substring is called a superstring.By the assumption of parsimony, a shortest possib原创 2022-07-07 16:58:08 · 194 阅读 · 0 评论 -
Rosalind Java|Longest Increasing Subsequence动态规划算法
Rosalind编程问题之计算集合中最长的递增元素子集。Problem:A subsequence of a permutation is a collection of elements of the permutation in the order that they appear. For example, (5, 3, 4) is a subsequence of (5, 1, 3, 4, 2).A subsequence is increasing if the elements of the原创 2022-06-22 20:40:30 · 125 阅读 · 0 评论 -
Rosalind Java|Counting Phylogenetic Ancestors
Rosalind编程问题之计算祖先数。Counting Phylogenetic AncestorsProblem:Even though a binary tree can include nodes having degree 2, an unrooted binary tree is defined more specifically: all internal nodes have degree 3. In turn, a rooted binary tree is such that onl原创 2022-05-23 17:19:09 · 137 阅读 · 0 评论 -
Rosalind Java|Locating Restriction Sites
Rosalind编程问题之检索限制性位点。Locating Restriction SitesProblem:A DNA string is a reverse palindrome if it is equal to its reverse complement. For instance, GCATGC is a reverse palindrome because its reverse complement is GCATGC. See Figure 2.Given: A DNA s原创 2022-05-22 20:39:30 · 155 阅读 · 0 评论 -
Rosalind Java|Consensus and Profile
Rosalind编程问题之统计多个序列中profile矩阵和consensus。Consensus and ProfileProblem:A matrix is a rectangular table of values divided into rows and columns. An m×n matrix has m rows and n columns. Given a matrix A, we write Ai,j to indicate the value found at the inte原创 2022-05-22 11:32:20 · 130 阅读 · 0 评论 -
Rosalind Java|Counting Subsets
Rosalind编程问题之计算集合的所有子集数。Counting SubsetsProblem:As illustrated in the biological introduction, we can use subsets to represent the collection of taxa possessing a character. However, the number of applications is endless; for example, an event in probab原创 2022-05-22 09:41:29 · 83 阅读 · 0 评论 -
Rosalind Java|Completing a Tree
“As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of t.原创 2022-05-20 18:45:02 · 207 阅读 · 0 评论 -
Rosalind Java|k-Mer Composition
Rosalind编程问题之统计DNA序列上由ACTG组成的K(4)-mers出现的次数。k-Mer CompositionProblem:For a fixed positive integer k, order all possible k-mers taken from an underlying alphabet lexicographically.Then the k-mer composition of a string s can be represented by an array A原创 2022-05-20 10:10:33 · 121 阅读 · 0 评论 -
Rosalind Java|Finding a Spliced Motif
Rosalind编程问题之查找两个序列由内含子分隔的共有motif。Ordering Strings of Varying Length LexicographicallyProblem:A subsequence of a string is a collection of symbols contained in order (though not necessarily contiguously) in the string (e.g., ACG is a subsequence of TATG原创 2022-05-19 09:47:27 · 205 阅读 · 0 评论 -
Rosalind Java|Ordering Strings of Varying Length Lexicographically
Rosalind编程问题之枚举字母的全部组合。与上一个问题有异曲同工之妙:Rosalind Java|Enumerating k-mers Lexicographically思路上可以一定程度借鉴这一篇博客。Ordering Strings of Varying Length LexicographicallyProblem:Say that we have strings s=s1s2⋯sm and t=t1t2⋯tn with m<n. Consider the substring t′原创 2022-05-18 10:16:18 · 74 阅读 · 0 评论 -
Rosalind Java|Enumerating k-mers Lexicographically
Rosalind编程问题之排列组合字母的K-mers。Enumerating k-mers LexicographicallyProblem:Assume that an alphabet A has a predetermined order; that is, we write the alphabet as a permutation A=(a1,a2,…,ak), where a1<a2<⋯<ak. For instance, the English alphabet is原创 2022-05-17 12:04:51 · 186 阅读 · 0 评论 -
Rosalind Java|Overlap Graphs
Rosalind编程问题之查找重叠区段。Overlap GraphsProblem:A graph whose nodes have all been labeled can be represented by an adjacency list, in which each row of the list contains the two node labels corresponding to a unique edge.A directed graph (or digraph) is a gr原创 2022-05-16 22:57:12 · 181 阅读 · 0 评论 -
Rosalind Java|Partial Permutations
Rosalind编程问题之部分排列。Partial PermutationsGiven: Positive integers n and k such that 100≥n>0 and 10≥k>0Sample input:21 7Return: The total number of partial permutations P(n,k), modulo 1,000,000Sample output:51200题目大意很容易理解:从一个含有n个数字的集合原创 2022-05-13 15:10:25 · 144 阅读 · 0 评论 -
Rosalind Java|Inferring mRNA from Protein
Rosalind编程问题之从蛋白序列推断可能的mRNA序列个数(并取余)。Inferring mRNA from ProteinGiven: A protein string of length at most 1000 aa.Sample input:MAReturn: The total number of different RNA strings from which the protein could have been translated, modulo 1,000,000.原创 2022-05-01 12:21:07 · 722 阅读 · 0 评论 -
Rosalind Java|Calculating Expected Offspring
Rosalind编程问题之计算杂交后代显性基因携带个体期望值。Calculating Expected OffspringGiven: Six nonnegative integers, each of which does not exceed 20,000. The integers correspond to the number of couples in a population possessing each genotype pairing for a given factor. In原创 2022-04-25 13:21:49 · 207 阅读 · 0 评论 -
Rosalind Java|Independent Alleles
Rosalind编程问题之计算等位基因杂合子比例。Independent AllelesProblemTwo events A and B are independent if Pr(A and B) is equal to Pr(A)×Pr(B). In other words, the events do not influence each other, so that we may simply calculate each of the individual probabilities se原创 2022-04-19 20:50:04 · 395 阅读 · 0 评论 -
Rosalind Java| Transitions and Transversions
Transitions and TransversionsProblemFor DNA strings s1 and s2 having the same length, their transition/transversion ratio R(s1,s2) is the ratio of the total number of transitions to the total number of transversions, where symbol substitutions are inferr原创 2022-04-06 17:22:40 · 386 阅读 · 0 评论 -
Rosalind Java| Computing GC Content
Rosalind编程问题之计算GC含量。Computing GC ContentProblemThe GC-content of a DNA string is given by the percentage of symbols in the string that are ‘C’ or ‘G’. For example, the GC-content of “AGCTATAG” is 37.5%. Note that the reverse complement of any DNA string原创 2022-03-24 11:12:10 · 208 阅读 · 0 评论 -
Rosalind Java| Mendel‘s First Law
Rosalind编程问题之孟德尔第一定律。这绝对是一道数学题。Mendel’s First LawProblemProbability is the mathematical study of randomly occurring phenomena. We will model such a phenomenon with a random variable, which is simply a variable that can take a number of different distin原创 2022-03-15 18:57:34 · 370 阅读 · 0 评论 -
Rosalind Java| RNA Splicing
Rosalind编程问题之剪切RNA。RNA SplicingProblemAfter identifying the exons and introns of an RNA string, we only need to delete the introns and concatenate the exons to form a new string ready for translation.Given: A DNA string s (of length at most 1 kbp) and原创 2022-03-13 21:35:02 · 126 阅读 · 0 评论 -
Rosalind Java|Enumerating Gene Orders
Rosalind编程问题之基因位置排列组合。Open Reading FramesProblemA permutation of length n is an ordering of the positive integers {1,2,…,n}. For example, π=(5,3,2,1,4) is a permutation of length 5.Given: A positive integer n≤7.Sample input:3Return: The total numb原创 2022-03-12 20:41:08 · 481 阅读 · 0 评论 -
Rosalind Java|Open Reading Frames
Rosalind编程问题之读取开放阅读框。Open Reading FramesProblemEither strand of a DNA double helix can serve as the coding strand for RNA transcription. Hence, a given DNA string implies six total reading frames, or ways in which the same region of DNA can be translate原创 2022-03-08 19:55:19 · 343 阅读 · 0 评论 -
Rosalind Java| Mortal Fibonacci Rabbits
兔兔那么可爱怎么会去世?Rosalind编程问题之计算斐波那契数列变式,江湖人称神兔也死问题。有关不死神兔问题可以参考这一篇文章:Rosalind Java| Rabbits and Recurrence Relations。Rabbits and Recurrence RelationsProblemRecall the definition of the Fibonacci numbers from “Rabbits and Recurrence Relations”, which follo原创 2022-03-01 19:41:05 · 202 阅读 · 0 评论 -
Rosalind Java| Rabbits and Recurrence Relations
兔兔那么可爱为什么要生兔兔?Rosalind编程问题之计算斐波那契数列,江湖也称不死神兔问题。Rabbits and Recurrence RelationsProblemA sequence is an ordered collection of objects (usually numbers), which are allowed to repeat. Sequences can be finite or infinite. Two examples are the finite sequen原创 2022-02-23 12:31:50 · 299 阅读 · 0 评论 -
Rosalind Java| Finding a Shared Motif
Rosalind编程问题之寻找共有的motif。Calculating Protein MassProblemIn a weighted alphabet, every symbol is assigned a positive real number called a weight. A string formed from a weighted alphabet is called a weighted string, and its weight is equal to the sum of t原创 2022-02-22 19:26:39 · 219 阅读 · 0 评论 -
Rosalind Java| Calculating Protein Mass
Rosalind编程问题之计算蛋白质分子量。Calculating Protein MassProblemIn a weighted alphabet, every symbol is assigned a positive real number called a weight. A string formed from a weighted alphabet is called a weighted string, and its weight is equal to the sum of the原创 2022-02-19 22:54:23 · 283 阅读 · 0 评论 -
Rosalind Java| Finding a Motif in DNA
Rosalind编程问题之查找motif。Finding a Motif in DNAProblemGiven two strings and , is a substring of if is contained as a contiguous collection of symbols in (as a result, must be no longer than ).The position of a symbol in a string is the total number o原创 2022-02-16 16:58:40 · 210 阅读 · 0 评论 -
Rosalind Java| Translating RNA into Protein
Rosalind编程问题之RNA翻译。Translating RNA into ProteinProblemThe 20 commonly occurring amino acids are abbreviated by using 20 letters from the English alphabet (all letters except for B, J, O, U, X, and Z). Protein strings are constructed from these 20 symbol原创 2022-02-15 10:12:50 · 337 阅读 · 0 评论 -
Rosalind Java| Counting Point Mutations
Rosalind编程问题之计数核酸序列突变数。Counting Point MutationsProblemGiven two strings s and t of equal length, the Hamming distance between s and t, denoted dH(s,t), is the number of corresponding symbols that differ in s and t. See Figure 2.原创 2022-02-13 08:51:45 · 324 阅读 · 0 评论 -
Rosalind Java| Complementing a Strand of DNA
Complementing a Strand of DNAProblemIn DNA strings, symbols ‘A’ and ‘T’ are complements of each other, as are ‘C’ and ‘G’.原创 2022-02-12 19:31:26 · 176 阅读 · 0 评论 -
Rosalind Java| Transcribing DNA into RNA
今天来分享Rosalind第二道题:转录Transcribing DNA into RNAProblemAn RNA string is a string formed from the alphabet containing ‘A’, ‘C’, ‘G’, and ‘U’.Given a DNA string t corresponding to a coding strand, its transcribed RNA string u is formed by replacing all occu原创 2022-02-11 11:03:49 · 296 阅读 · 0 评论 -
Rosalind Java| Counting DNA Nucleotides
RosalindRosalind是一个生物信息编程学习网站。抛出了一系列生物学问题,引导使用者通过编程语言解决。网站官方推荐使用python解决,python得益于丰富的开源包,其解决方法在CSDN中也多有涉及。小编使用的主语言是java,因此简单通过CSDN社区进行Java学习笔记记录,不足之处也请大家多多指点~先来看一下问题描述:Counting DNA NucleotidesProblemA string is simply an ordered collection of symbols原创 2022-02-10 20:27:39 · 700 阅读 · 0 评论