Exclusive sequences of different genomes.
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.
Mitrofanov
Sergey I
SI
Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia. mitroser04@mail.ru
Panchin
Alexander Y
AY
Spirin
Sergei A
SA
Alexeevski
Andrei V
AV
Panchin
Yuri V
YV
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D016678:Genome / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*