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Given a multiFASTA file and for each sequence, shuffle middle part of the sequence leaving the flanks intact and the opposite

Hello all,

Is there any tool which, given a multiFASTA file and for each sequence, shuffles middle part of the sequence leaving the flanks (user specifies them) intact and the opposite?

Thanks, Dimitris

sequence shuffle bedtools genome
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written by Dimitris Polychronopoulos • Dimitris Polychronopoulos

Shuffling means randomly permute nucleotides? How are the flanks determined? By size or by length?

This sounds like something that needs a specific script, not common enough for an existing tool, although I might be wrong since the plethora of existing tools is enormous. The solution would be quite easy to script in python (and other languages but I'm a python-guy so I'll say python). Are you familiar with programming?

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written by WouterDeCoster WouterDeCoster

What would bethe difference between size and length in this context? I know R but thought that there might exist already a function within a package that could do it

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written by Dimitris Polychronopoulos • Dimitris Polychronopoulos

I meant by sequence or by length, but size was a typo.

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written by WouterDeCoster WouterDeCoster

1 answer

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks Pierre. What I mean is that for every sequence in the multiFASTA file, shuffle the middle part and keep flanks intact. I have edited the question so that it is more clear

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written by Dimitris Polychronopoulos • Dimitris Polychronopoulos

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