When there are no duplications, rename the sequences into permutations. When there are no duplications, rename the sequences into permutations.
We study the problem of sorting binary sequences and permutations by length-weighted reversals. We consider a wide class of cost functions, namely f () = α for all α ≥ 0, where is the length of the reversed subsequence. We present tight or nearly tight upper and lower bounds on the worst-case cost of sorting by reversals. Then we develop algorithms to… (More)
We study the problem of sorting integer sequences and permutations by length-weighted reversals. We consider a wide class of cost functions, namely <i>f(l)</i> = <i>l</i><sup>α</sup> for all α ≥ 0, where <i>l</i> is the length of the reversed subsequence. We present tight or nearly tight upper and lower bounds on the worst-case cost of… (More)
We present MAGIC, an integrative and accurate method for comparative genome mapping. Our method consists of two phases: preprocessing for identifying "maximal similar segments," and mapping for clustering and classifying these segments. MAGIC's main novelty lies in its biologically intuitive clustering approach, which aims towards both calculating… (More)
Comparing genomes is an essential preliminary step to solve many problems in biology. Matching long similar segments between two genomes is a precondition for their evolutionary, genetic, and genome rearrangement analyses. Though various comparison methods have been developed in recent years, a quantitative assessment of their performance is lacking. Here,… (More)
Selenocysteine is the 21th amino acid, which occurs in all kingdoms of life. Selenocysteine is encoded by the STOP-codon UGA. For its insertion, it requires a specific mRNA sequence downstream the UGA-codon that forms a hairpin like structure (called Sec insertion sequence (SECIS)). We consider the computational problem of generating new amino acid… (More)
A new problem in phylogenetic inference is presented, based on recent biological findings indicating a strong association between reversals (i.e., inversions) and repeats. These biological findings are formalized here in a new mathematical model, called repeat-annotated phylogenetic trees (RAPT). We show that, under RAPT, the evolutionary process--including… (More)
Phylogenetic inference is an essential problem in evolutionary studies. It is being addressed by a wide class of methods, ranging from those based on phenotypic morphologies to others using various genotypic mutations. Yet, they all lead to results which are potentially both ambiguous and biologically inconclusive. In this paper, a novel approach is… (More)