5uperb0y's blog

給定一 FASTA 檔案，內含數條由 A、C、G、T 組成的字串，求這些字串共享的最長子字串。

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 substring of “ACGTACGT” and “AACCGTATA”, but it is not as long as possible; in this case, “CGTA” is a longest common substring of “ACGTACGT” and “AACCGTATA”.
Note that the longest common substring is not necessarily unique; for a simple example, “AA” and “CC” are both longest common substrings of “AACC” and “CCAA”.

Given: A collection of k (k≤100) DNA strings of length at most 1 kbp each in FASTA format.

Return: A longest common substring of the collection. (If multiple solutions exist, you may return any single solution.)

(https://rosalind.info/problems/lcsm/)

Problem

給定字串 s 與 t，其中 t 的長度小於等於 s，求 s 與 t 一致之子序列的起始位置。

Given: Two DNA strings s and t (each of length at most 1 kbp).

Return: All locations of t as a substring of s.

(https://rosalind.info/problems/subs/)

給定字符序列 $\mathscr{A}$，求由這些字符組成且長度小於等於 k 的所有字串。這些字串須依照 $\mathscr{A}$ 字典序排列。

Given: A permutation of at most 12 symbols defining an ordered alphabet $\mathscr{A}$ and a positive integer n (n≤4).

Return: All strings of length at most n formed from $\mathscr{A}$, ordered lexicographically. (Note: As in “Enumerating k-mers Lexicographically”, alphabet order is based on the order in which the symbols are given.)

(https://rosalind.info/problems/lexv/)

給定字符序列 $\mathscr{A}$，求由這些字符組成且長度為 k 的所有字串。這些字串須依照 $\mathscr{A}$ 字典序排列。

Given: A permutation of at most 12 symbols defining an ordered alphabet $\mathscr{A}$ and a positive integer n (n≤4).

Return: All strings of length at most n formed from $\mathscr{A}$ , ordered lexicographically. (Note: As in “Enumerating k-mers Lexicographically”, alphabet order is based on the order in which the symbols are given.)

(https://rosalind.info/problems/lexv/)

給定一正整數 n，求包含數字 1 到 n 與 -1 到 -n 的所有可能數列與其總數。

A signed permutation of length n is some ordering of the positive integers {1,2,…,n} in which each integer is then provided with either a positive or negative sign (for the sake of simplicity, we omit the positive sign). For example, π=(5,−3,−2,1,4) is a signed permutation of length 5

Given: A positive integer n≤6

Return: The total number of signed permutations of length n, followed by a list of all such permutations (you may list the signed permutations in any order).

給定一正整數 n，求包含數字 1 到 n 的所有可能數列與其總數。

A 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 .

Return: The total number of permutations of length n , followed by a list of all such permutations (in any order).

(https://rosalind.info/problems/perm/)

給定兩等長字串 s 和 t，計算兩者的 Hamming distance dH(s,t)

Given: Two DNA strings s and t of equal length (not exceeding 1 kbp).

Return: The Hamming distance dH(s,t).

(https://rosalind.info/problems/hamm/)

本文純粹是技術問題。我之前以 Qiime2 外掛的 DADA2 處理已切除轉接子的 16S rRNA 基因序列 (V4 region) 時，因為以下錯誤而中斷了執行四天的程式。

1

Plugin error from dada2: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

給定 DNA 序列，回傳其反向互補序列。

Given: A DNA string s of length at most 1000 bp.

Return: The reverse complement sc of s.

(https://rosalind.info/problems/revc/)

小說¹是以主角朋友的紀錄呈現。開頭場景類似電影《來自地球的人》，是一場舉行在主角家裡的沙龍。當一夥人正熱烈討論著時空本質時，主角現身向他們展示了正在打造的時光機器。不過要到主角衣衫襤褸，渾身是傷地出現在再次造訪的友人面前，讀者才得以讀到由敘事者轉述，主角經歷的未來冒險。