• 1
  • 2
  • 5
  • 6
  • 7
  • 8
  • 9
  • 3
  • 4

“School of Biological”

Back to Papers Home
Back to Papers of School of Biological

Paper   IPM / Biological / 13197
School of Biological Sciences
  Title:   Construction Of Random Perfect Phylogeny Matrix
1 . M. Sadeghi.
2 . H. Pezeshk.
3 . C. Eslahchi.
4 . S. Ahmadian.
5 . S. Mah Abadi.
  Status:   Published
  Journal: Advances and Applications in Bioinformatics and Chemistry
  Vol.:  3
  Year:  2010
  Pages:   89-96
  Supported by:  IPM
Interest in developing methods appropriate for mapping increasing amounts of genome-wide molecular data are increasing rapidly. There is also an increasing need for methods that are able to efficiently simulate such data.
Patients and methods
In this article, we provide a graph-theory approach to find the necessary and sufficient conditions for the existence of a phylogeny matrix with k nonidentical haplotypes, n single nucleotide polymorphisms (SNPs), and a population size of m for which the minimum allele frequency of each SNP is between two specific numbers a and b.
We introduce an O(max(n2, nm)) algorithm for the random construction of such a phylogeny matrix. The running time of any algorithm for solving this problem would be Ω (nm).
We have developed software, RAPPER, based on this algorithm, which is available at http://bioinf.cs.ipm.ir/softwares/RAPPER

Download TeX format
back to top
Clients Logo
Clients Logo
Clients Logo
Clients Logo
Clients Logo
Clients Logo
Clients Logo
Clients Logo
scroll left or right