Analysing miRNA expression in cancers

MiRNAs are a class of small RNAs that when expressed usually down regulates the expression of its target transcript by binding to it and causing it to degrade or inhibiting it from being translated. There has been a lot of interest in studying the expression pattern of miRNAs, especially in relation to cancer, since their...

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RNAfold

RNAfold is a program that calculates secondary structures of RNAs. RNAfold reads RNA sequences from stdin, calculates their minimum free energy (mfe) structure and prints to stdout the mfe structure in bracket notation and its free energy. My understanding is that the lowest energy structure i.e. minimum free energy, is the most thermodynamical stable one....

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Why miRNA are 22 or 23 nucleotides long

Late last year I mapped random sized DNA sequences back to the genome. The purpose was simply to see how long sequenced reads needed to be before they could be uniquely mapped to the genome. I couldn't find the statistics on this, so I just did it myself. I didn't dwell on the results too...

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Using blat to map short RNAs

Updated on 2013 November 5th to include mapping of piRNAs I still use blat as my multi-purpose alignment tool despite it being developed over 10 years ago. For those needing a simple introduction to blat, see my using blat post. Now I was wondering if blat could aligned short RNAs; the definition of short RNAs...

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