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wiki:2016substitutions [2017/09/06 09:00]
tai
wiki:2016substitutions [2017/09/07 08:53] (current)
tai
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 |%%[0-9]%% | a character class, any number | |%%[0-9]%% | a character class, any number |
 |%%[a-z]%% | a character class, any letter | |%%[a-z]%% | a character class, any letter |
-|%%|%% | use to match something on the left or something on the right e.g. DNA%%|%%RNA |+|%%|%% | use to match something on the left or something on the right e.g. DNA%%|%%RNA ​(use egrep)|
 |%%\\n%% | the first back slash negates the second backslash, useful if you really want to search for something like \n and not a new line.| |%%\\n%% | the first back slash negates the second backslash, useful if you really want to search for something like \n and not a new line.|
  
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 **1.** Obtain all miRNA sequences in fasta format from the mirbase download page.  The file is called **mature.fa**. \\ \\ **1.** Obtain all miRNA sequences in fasta format from the mirbase download page.  The file is called **mature.fa**. \\ \\
-**2.** Extract all worm (C. elegans), fly (D. malanogaster),​ and human (H. sapien) miRNAs preserving fasta format. \\ \\+**2.** Extract all worm (C. elegans), fly (D. malanogaster),​ and human (H. sapiens) miRNAs preserving fasta format ​(egrep is needed when matching either or). \\ \\
 **3.** Use **tr** to convert all RNA sequences to DNA sequences. \\ \\ **3.** Use **tr** to convert all RNA sequences to DNA sequences. \\ \\
 **4.** Determine how many miRNAs start with each possible 5' nucleotide (A, C, G, T) - what is the most common 5' nt? \\ \\ **4.** Determine how many miRNAs start with each possible 5' nucleotide (A, C, G, T) - what is the most common 5' nt? \\ \\
 **5.** Determine how many miRNAs are 20, 21, 22, 23, and 24 nt.  What is the most common length of miRNAs? \\ \\ **5.** Determine how many miRNAs are 20, 21, 22, 23, and 24 nt.  What is the most common length of miRNAs? \\ \\
 **6.** Extract all potential let-7 miRNA family members using **grep**, preserving the fasta format. ​ miRNA families are determined by their seed sequence, positions 2-8 of the mature miRNA. ​ The seed sequence of let-7 is: GAGGTAG. \\ \\ **6.** Extract all potential let-7 miRNA family members using **grep**, preserving the fasta format. ​ miRNA families are determined by their seed sequence, positions 2-8 of the mature miRNA. ​ The seed sequence of let-7 is: GAGGTAG. \\ \\
wiki/2016substitutions.txt ยท Last modified: 2017/09/07 08:53 by tai