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Comparative analysis of predicted DNA secondary structures infers complex human centromere topology

In this repository, we showcase the scripts and tools used in our analysis. Below are the details of the folders and their contents:

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Folders

There are three folders in this github repository:

  1. Free Energy Evaluation/ - This corresponds to the usage of the tool RNAfold to predict the secondary structures of DNA obtained from various regions of the centromere.
  2. Non-B DNA motif finder/ - This folder contains information regarding the usage of the tool nBMST (non-B DNA Motif search tool) to determine the non-B DNA motifs presence in the centromeric regions considered.
  3. Dyad Density Evaluation/ - The usage of the tool EMBOSS Palindrome to evaluate the dyad density in the peri/centromeric regions is demonstrated in this folder.