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CLIP-seq 101

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A little book about CLIP-seq

By Yun Yan. Feel free to email me:, please, with the polyA tail removed.

This is an overview, glimpse, simple introduction to CLIP-seq. This little book would cover the brief history related to biochemistry; what data and information you could get out of CLIP-seq; how to analyze those data. In particular how computer science contribute to robust data analysis, including hidden Markov model, random forest, SVM, etc.

Hopefully this book would build a bridge between biologists and geeky computational scientists, at least in RNA-protein interaction research fields. After reading this book, bio-readers would have clearer concept about how the raw data produced by your efforts would be literally cooked as findings with scientific meanings. On the other hand computational scientists would not only learn to appreciate the underlying biological mysteries but also make the link between figuring out computational algorithms and solving biological problems more tight.

The on-line html version of this book is deployed at and created by using Sphinx. Readthedocs automatically genreate the pdf file of this booklet though it is not perfect as custom Tex. It could be downloaded here.

Book source at Github:


  • Apr 17 2014. Questions on PTB transition prob matrix. Waiting for feedback from authors.
  • Apr 14 2014. PTB HMM reproducbile.
  • Apr 12 2014. Selecting most possible path by emunerating.
  • Apr 11 2014. Section 3.1 HMM: new source code for generating sequence
  • Apr 9 2014. Working on HMM introduction. So far “generat sequence”.