Complexity Measures for Gene Assembly

The process of gene assembly in ciliates is a fascinating example of programmed DNA manipulations in living cells. Macronuclear genes are split into coding blocks (called MDSs), shuffled and separated by non-coding sequences to form micronuclear genes. Assembling the coding blocks from micronuclear genes to form functional macronuclear genes is facilitated by an impressive in-vivo implementation of the linked list data structure of computer science. Complexity measures for genes may be defined in many ways, including the number of MDSs, the number of loci, etc. We take a different approach in this paper and propose four complexity measures for genes in ciliates, based on the 'effort' required to assemble the gene. We consider: (a) the types of operations used in the assembly, (b) the number of operations used in the assembly, (c) the length of the molecular folds involved, and (d) the length of the shortest possible parallel assembly for that gene. "One of the oldest forms of life on Earth has been revealed as a natural born computer programmer."