Please use this identifier to cite or link to this item: http://hdl.handle.net/10397/25884
Title: Cross chromosomal similarity for DNA sequence compression
Authors: Wu, CPP
Law, NF 
Siu, WC 
Keywords: DNA
Sequence
Chromosome
Prediction
S. cerevisiae
Issue Date: 2008
Publisher: Biomedical Informatics Publishing Group
Source: Bioinformation, 2008, v. 2, no. 9, p. 412-416 How to cite?
Journal: Bioinformation 
Abstract: Current DNA compression algorithms work by finding similar repeated regions within the DNA sequence and then encoding these regions together to achieve compression. Our study on chromosome sequence similarity reveals that the length of similar repeated regions within one chromosome is about 4.5% of the total sequence length. The compression gain is often not high because of these short lengths. It is well known that similarity exist among different regions of chromosome sequences. This implies that similar repeated sequences are found among different regions of chromosome sequences. Here, we study cross-chromosomal similarity for DNA sequence compression. The length and location of similar repeated regions among the sixteen chromosomes of S. cerevisiae are studied. It is found that the average percentage of similar subsequences found between two chromosome sequences is about 10% in which 8% comes from cross-chromosomal prediction and 2% from self-chromosomal prediction. The percentage of similar subsquences is about 18% in which only 1.2% comes from self-chromosomal prediction while the rest is from cross-chromosomal prediction among the 16 chromosomes studied. This suggests the importance of cross-chromosomal similarities in addition to self-chromosomal similarities in DNA sequence compression. An additional 23% of storage space could be reduced on average using self-chromosomal and cross-chromosomal predictions in compressing the 16 chromosomes of S. cerevisiae.
URI: http://hdl.handle.net/10397/25884
ISSN: 0973-2063
Appears in Collections:Journal/Magazine Article

Access
View full-text via PolyU eLinks SFX Query
Show full item record

Page view(s)

35
Last Week
0
Last month
Checked on Sep 25, 2017

Google ScholarTM

Check



Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.