Speaker: Jin Jun
Day:  Wednesday, 10/12/2005
Room: ITEB 201
Time: 3:30pm
Title: Finding founder sequences

Abstract:
In this paper the author suggested a new approach to find 
haplotype blocks (or motifs) and novel algorithms to reconstruct 
founder sequences from given haplotypes (or sequences). 
The structure of haplotypes (or DNA sequences) is helpful to 
the association study of genetic diseases. The previous researches 
about haplotype blocks are based on global structure of crossover, 
which assumed that there is no restriction on recombination and 
the population is stable in terms of evolution. 
The author used mosaic-like structure for the population assumed 
to have evolved as an isolate, founded some generations ago 
by a small number of settlers. Then the sequences in given sequences 
should be a result of recombinations of the founder sequences.
The problem, now, is to find a set of founder sequences such that 
given sequences can be composed from fragments taken from 
the founder sequences. He gives polynomial-time algorithm 
for some special cases as well as a general solution by dynamic programming. 

Esko Ukkonen, Finding founder sequences from a set of recombinants, 
Proc. Algorithms in Bioinformatics (WABI-2002), Lecture Notes in 
Computer Science 2452, pp. 277-286, Springer 2002.