Wednesday November 15th, 2006
CSE Room 305
12:00 - 1:00 PM
|
Multiple
Sequence Alignment Solutions and Applications |
|
Xu Zhang |
|
The
rapid progress of computer science, as an assistant to biology led to the
field of bioinformatics. In this area, multiple sequence alignment (MSA) is a
fundamental problem. MSA is widely used in many applications such as protein
structure prediction, phylogenetic analysis, identification of conserved motifs, protein classification
and genome primer identification. MSA
is a challenging problem for finding the multiple sequence alignment that
maximizes the SP (Sum-of-Pairs) score is NP-complete. Also, finding an
alignment that is biologically meaningful is not trivial since the SP score
may not reflect the biological significances. The presentation addresses
these problems. More specifically we consider three problems. First, we propose
to apply secondary structure information of residues to build a biological
meaningful alignment. Second we develop an efficient algorithm to optimize
the SP score of MSA. The third problem addresses how multiple sequences can
be used for primer prediction. |
For
upcoming talks, visit http://www.cise.ufl.edu/dbcenter/seminar.shtml