Chapter 9: Bioinformatic Analysis of Nanopore Data

Earlier chapters described how a MinION can determine base sequences of single-stranded nucleic acid molecules (DNA or RNA) as they are translocated through a nanopore by an applied potential. The translocation rate is controlled by a helicase enzyme that rachets the strand through the pore at ∽450 bases per second (b/s). The potential, or voltage applied across the membrane, produces an ionic current that flows through the pore along with the nucleic acid. The current is modulated by combinations of nucleobases in the nucleic acid called kmers, and each kmer has a specific effect on the ionic current. The ionic current modulations can be related to specific kmers which allows the sequence of bases in the nucleic acid to be determined…