Drawing Alternative Splicing Graphs

Alternative splicing of a single pre-mRNA can give rise to different mRNA transcripts. Alternative splicing of premessenger RNA is an important layer of gene expression regulation in eukaryotic cell. Consequently, alternative splicing is an important mechanism for generating protein diversity from a single gene. Due to all these important aspects of genomic alternative splicing mechanism that produces different mRNA’s, biologists require means of analyzing and visualizations of the alternative splicing forms. In this paper, we consider ways of drawing a given alternative splicing graph on the plane. Given an alternative splicing graph G = (V,E), here in this paper we show that computing the crossing number of a given upper drawing ASG can be done in O(|E| log |E|) time. The optimal (fewest crossing) drawing of alternative splicing graphs is related to the long known difficult problem of crossing number. Here we propose an efficient branch-and-bound recursive algorithm with heuristic searching strategy. Some experimental results are also discussed in the paper.