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Molecular & Biochemical Parasitology 118 (2001) 175186 Discovering patterns in Plasmodium falciparum genomic DNA
 

Summary: Molecular & Biochemical Parasitology 118 (2001) 175186
Discovering patterns in Plasmodium falciparum genomic DNA
Linda Stern a,
*, Lloyd Allison b
, Ross L. Coppel c
, Trevor I. Dix b
a
Department of Computer Science and Software Engineering, The Uni6ersity of Melbourne, Melbourne, Victoria 3010, Australia
b
School of Computer Science and Software Engineering, Monash Uni6ersity, Clayton, Victoria 3800, Australia
c
Department of Microbiology, Monash Uni6ersity, Clayton, Victoria 3800, Australia
Abstract
A method has been developed for discovering patterns in DNA sequences. Loosely based on the well-known Lempel Ziv model
for text compression, the model detects repeated sequences in DNA. The repeats can be forward or inverted, and they need not
be exact. The method is particularly useful for detecting distantly related sequences, and for finding patterns in sequences of biased
nucleotide composition, where spurious patterns are often observed because the bias leads to coincidental nucleotide matches. We
show here the utility of the method by applying it to genomic sequences of Plasmodium falciparum. A single scan of chromosomes
2 and 3 of P. falciparum, using our method and no other a priori information about the sequences, reveals regions of low
complexity in both telomeric and central regions, long repeats in the subtelomeric regions, and shorter repeat areas in dense

  

Source: Allison, Lloyd - Caulfield School of Information Technology, Monash University

 

Collections: Computer Technologies and Information Sciences