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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Mapping long reads with Bowtie

Just a simple test to see if Bowtie can map long reads. Why? Well because Bowtie is fast, so I want to see if I can also use it as a general purpose aligner. In a previous post I was characterising the mapability of the genome. From this I selected a portion of the genome...

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