“School of Biological Sciences”

Back to Papers Home
Back to Papers of School of Biological Sciences

Paper   IPM / Biological Sciences / 13197
School of Biological Sciences
  Title:   Construction Of Random Perfect Phylogeny Matrix
  Author(s): 
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
  Abstract:
Purpose
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.
Results
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).
Conclusion
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
Clients Logo
Clients Logo
scroll left or right