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Hyrum Carroll

Friday, March 14

5-th floor conference room

2PM

 

Codon Sequence Alignment With Physicochemical Properties

 

Abstract:

Researchers use multiple sequence alignment algorithms to detect motifs in genetic sequences and identify targets for drug development.  
Current algorithms use DNA or amino acids as the basic unit of data.  Codons have more information than either DNA or amino acids.  
For this dissertation we propose a novel three-phase approach to multiple sequence alignments of protein-coding DNA.  In the first phase, 
we determine the secondary structure assignments for each sequence.  Next, we identify highly conserved regions in the sequences to use 
as constraints.  Finally, we align the sequences as codons using contextual substitution matrices.  This alignment is constrained by 
the secondary structure elements and the conserved regions.   This approach results in alignments that are more accurate and useful 
for drug development and other medical uses.