Burrows-Wheeler transform
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3 months ago
Balqees • 0

Hi, I want to ask about BWT for DNA sequence compression. In the first step, which language is better to implement BWT? Python or R? And why?

What is the difference in left rotation and right rotation? I rotated my sequence manually in both directions, it gave me two different BWT output ( two different sequences) and when I inverse both of them return to the original sequence, So both ways are right and work!! But I want to know which rotation direction is better to compress the DNA sequence. Is the rotation side effect the sensitivity? Or the preference. And how can I test it ?

Thank you

Python BWT DNA • 595 views
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which language is better to implement BWT?

please define "better" ? better for what ? speed ?

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Yes, for speed

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C/C++ are the best for speed. If you can rely on C++ based Python libraries, it might be faster. Why not develop it both ways and run benchmarks? Or look for a paper that already did it?

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I run in it in Python, I am not familiar to C++. But I will look for papers . Thank u

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I meant Python and R, not C++. It might be a fun learning exercise to do it in two different approaches - by pure programming in Python and using vectorized functions in R.

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Why does this sound like homework?

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