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how to permute randomly a miRNA sequence?

how to permute randomly a miRNA sequence? - RNA Forum

how to permute randomly a miRNA sequence? - RNA Forum. Discuss RNA including mRNA structure and function, rRNA, tRNAs, and the biochemistry of other RNA molecules.


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  #1  
Old 12-24-2011, 09:36 PM
Pipette Filler
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Question how to permute randomly a miRNA sequence?



Hello
I have a number of miRNA sequences and i need to permute each sequence randomly.does anyone know a tool or an algorithm to perform such task?

thnaks in advance.
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Old 12-25-2011, 04:35 PM
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Default Re: how to permute randomly a miRNA sequence?

I am not sure if I understand correctly details of your problem. If you want to permute the sequence in the computer, I would program it in Microsoft Excel. You can generate the random integer number from the set of 1, 2, 3, and 4 using the following formula,

=ROUND((RAND()*4+0.5),0)

You can use the IF selection statement to convert the random number to the base. For example,

=IF(A3=1,"A",IF(A3=2,"C",IF(A3=3,"G",IF(A3=4,"U"," "))))

where the random number is in the cell A3 of the Excel sheet. If you place your sequence in the cell C3, you can then randomly pick the position in the sequence with =ROUND((RAND()*LEN(C3)+0.5),0) formula in the cell D1.

The mutated sequence can be obtained with the =REPLACE(C3,D3,1,B3) function.

I attached the Excel file that can do that. You may need to turn off automatic Excel recalculation if you do not want the results to change every time you open the file or modify the sheet.

Good luck!

Richard Owczarzy
www dot owczarzy dot net
Attached Files
File Type: zip SequenceMutate.zip (7.4 KB, 2 views)
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Old 12-25-2011, 10:35 PM
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Default Re: how to permute randomly a miRNA sequence?

hi rowczarzy

Thanks very much for the reply.i think you got my question right.for instance i have a miRNA sequence of this order AUGGAACAU,,now i want to generate a random sequence with the same nucleotides e.g: GAGACUAUA

i hope ur excel algorithm can do that.am going to try that right away and get back to you.thanks again for your help.
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Old 12-26-2011, 03:29 PM
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Default Re: how to permute randomly a miRNA sequence?

@rowczarzy

your excel programm mutates the sequence at a random position.Maybe i am not expressing my problem well,but that is not what i actually want to do.like i said in my previous post, i have for instance a miRNA sequence AUGGAACAU,,now i want to generate a random sequence with the same nucleotides composition as the original miRNA e.g: GAGACUAUA.i hope you understand what i mean.please help me of you can.
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Old 12-26-2011, 04:42 PM
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Default Re: how to permute randomly a miRNA sequence?

That is a little bit different task. It is easier to do it in a custom VBA function. I created the StringPermut function. You can see it in the attached Excel when you press Alt-F11. To rerun the function and make new permutations, press Ctrl-Alt-F9. This will do full Excel recalculation.

Enjoy!

Richard Owczarzy

----------------------------------------------------------------------------
Option Explicit

Function StringPermut(ByVal Seq As String) As String

' function permutate characters in string

Dim arrStr() As String
Dim OutStr As String
Dim Lseq As Long
Dim i As Long
Dim ipick As Long

StringPermut = ""
Lseq = Len(Seq)

If (Lseq < 1) Then
Return
End If

ReDim arrStr(1 To Lseq)
OutStr = ""
Randomize

' Split inputed sequence into array of characters
For i = 1 To Lseq
arrStr(i) = Mid(Seq, i, 1)
Next i

Do
' Choose randomly one character from the set and copy it to output array
ipick = Int((Lseq - 1 + 1) * Rnd + 1)
OutStr = OutStr & arrStr(ipick)
' Remove the selected ipick character from the set that I will use to select the next character
' Decrease the set by 1 character
Lseq = Lseq - 1
For i = ipick To Lseq
' ipick character is overwritten with the next character
arrStr(i) = arrStr(i + 1)
Next i
Loop While Lseq >= 1
StringPermut = OutStr

End Function ' StringPermut
Attached Files
File Type: zip SequencePermutate.zip (14.3 KB, 2 views)
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  #6  
Old 01-16-2012, 09:43 AM
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Default Re: how to permute randomly a miRNA sequence?

@rowczarzy

Thanks so much.it s working perfectly..
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Old 08-26-2012, 07:30 AM
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Default Re: how to permute randomly a miRNA sequence?

i have for instance a miRNA sequence AUGGAACAU,,now i want to generate a random sequence with the same nucleotides composition as the original miRNA e.g: GAGACUAUA
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