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We consider the problem of sorting linear and circular permutations and 0/1 sequences by reversals in a length-sensitive cost model. We extend the results on sorting by length-weighted reversals in two directions: we consider the signed case for linear sequences and also the signed and unsigned cases for circular sequences. We give lower and upper bounds as… (More)

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)

- Michael A. Bender, Dongdong Ge, Simai He, Haodong Hu, Ron Y. Pinter, Steven Skiena +1 other
- SODA
- 2004

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)

- Firas Swidan, Eduardo P. C Rocha, Michael Shmoish, Ron Y Pinter
- PLoS Computational Biology
- 2006

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)

- Rolf Backofen, N S Narayanaswamy, Firas Swidan
- In silico biology
- 2002

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)

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)

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)

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