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J Bioinform Comput Biol. 2010 Jun;8(3):519-34.

Exclusive sequences of different genomes.

Author information

1
Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia. mitroser04@mail.ru

Abstract

We studied the distribution of 1-7 bp words in a dataset that includes 139 complete eukaryotic genomes, 33 masked eukaryotic genomes and coding regions from 35 genomes. We tested different statistical models to determine over- and under-represented words. The method described by Karlin et al. has the strongest predictive power compared to other methods. Using this method we identified over- and under-represented words consistent within a large array of taxonomic groups. Some of those words have not yet been described as exclusive. For example, CGCG is over-represented in CG-deficient organisms. We also describe exceptions for widely known exclusive words, such as CG and TA.

PMID:
20556860
DOI:
10.1142/S0219720010004719
[Indexed for MEDLINE]

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