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
