Title: Department of Computer Science Seminar
Date:  Wednesday, 28 May 2003
Time:  4:00 pm to 5:00 pm
Venue: Room N101, CSIT Building [108]


Title:   Normalization of Sequence Alignment Scores

Speaker: Dr Hilary Booth (Centre for Bioinformation Science
         (CBiS) at ANU)


Abstract:
  We describe a normalization procedure for the score of a
  pairwise alignment of two biological sequences and an algorithm
  (POZITIV) that finds the normalized score efficiently. Designed
  to overcome the bias due to the composition of the alignment,
  the normalized score (which we call the POZ score) measures the 
  distance (in standard deviations) between Smith-Waterman (S-W)
  score of the aligned letters and  the mean value of all other
  S-W scores obtained by a permutation of either sequence. Unlike
  the usual Z-score calculation used in sequence alignment, the
  mean and standard deviation are taken without realigning the
  permuted sequences.  We demonstrate that calculating the mean
  and standard deviation in this way enables us to calculate
  exactly and in two steps, the first being O(N) time, where N is
  the length of the sequence, the second in a fixed number of
  calculations i.e. in O(1) time.


Biography:
  Ordinary degree in mathematical physics at the University of
  Adelaide. Took 10 year break from academia and exhibited own
  artwork in Australia Europe and UK (and had kids). Came back
  to do a PhD at University of New England (UNE), topic: Nonlinear
  partial differential equations of quantum mechanics.
  Lectured at UNE, lectured for 3 years at University of Adelaide
  (teaching maths to big engineering classes), took up a postdoc at
  the CMA here at ANU. Got involved in the Science Festival of 2001
  on the theme of bioinformatics. Found it so interesting that I
  said yes when they offered me a post doc followed by a research
  job. Been in bioinformatics for 2 years.

  Still have sideline in art. Designed the cover for the Aust Maths
  Society's Journals, images for MSI etc.


URL: http://cs.anu.edu.au/lib/seminars/seminars03/dept20030528