Question

Problem-3 This problem is referred to as Exon chaining in bioinformatics. Each gene corresponds to a subre- gion of the overall genome (the DNA sequence); however, part of this region might be "junk DNA”. Frequently, a gene consists of several pieces called exons, which are separated by junk fragments called introns. This complicates the process of identifying genes in a newly sequenced genome. Suppose we have a new DNA sequence and we want to check whether a certain gene (a string) is present in it. Because we cannot hope that the gene will be a contiguous subsequence, we look for partial matches, fragments of DNA that are also present in the gene (actually, even these partial matches will be approximate, not perfect). We then attempt to assemble these fragments. Let x[1...n] denote the DNA sequence. Each partial match can be represented by a triple (li; ri;wi), where x[li... ri] is the fragment and wi is a weight representing the strength of the match it might be a local alignment score or some other statistical quantity). Many of these potential matches could be false, so the goal is to find a subset of the triples that are consistent (nonoverlapping) and have a maximum total weight. Show how to do this in O(n + m), where m is the number of partial matches.

Answer 1

Exon Chaining assumes the positions and weights of exons are pre-defined. Goal: Align entire human and mouse genomes. Predict genes in both sequences simultaneously as chains of aligned blocks (exons). This approach does not assume any annotation of either human or mouse genes

An Introduction to Bioinformatics AlgorithmsUsing Known Genes to Predict New Genes•Some genomes may be very well-studied, with many genes having been experimentally verified.•Closely-related organisms may have similar genes•Unknown genes in one species may be compared to genes in some closely-related species