Approximating the Spanning Star Forest Problem and Its Application to Genomic Sequence Alignment

  • Authors:
  • C. Thach Nguyen;Jian Shen;Minmei Hou;Li Sheng;Webb Miller;Louxin Zhang

  • Affiliations:
  • ncthach@cs.washington.edu;js48@txstate.edu;mhou@cs.niu.edu;lsheng@math.drexel.edu;webb@bx.psu.edu;matzlx@nus.edu.sg

  • Venue:
  • SIAM Journal on Computing
  • Year:
  • 2008

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Abstract

This paper studies the algorithmic issues of the spanning star forest problem. We prove the following results: (1) There is a polynomial-time approximation scheme for planar graphs; (2) there is a polynomial-time $\frac{3}{5}$-approximation algorithm for graphs; (3) it is NP-hard to approximate the problem within ratio $\frac{259}{260} + \epsilon$ for graphs; (4) there is a linear-time algorithm to compute the maximum star forest of a weighted tree; (5) there is a polynomial-time $\frac{1}{2}$-approximation algorithm for weighted graphs. We also show how to apply this spanning star forest model to aligning multiple genomic sequences over a tandem duplication region.