A study of the repetitive structure and distribution of short motifs in human genomic sequences

Authors:
Abanish Singh;Cedric Feschotte;Nikola Stojanovic
Affiliations:
Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX 76019, USA.;Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA.;Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, TX 76019, USA
Venue:
International Journal of Bioinformatics Research and Applications
Year:
2007

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Abstract

Over the last several years the search for functional genomicelements by exploiting motif over-representation becameincreasingly popular. However, about half of the human genome isrepetitive, and that is also the case with most higher eukaryotes.In this study we have shown that in addition to these knownrepeats, human sequences feature many short over-representedmotifs, and that their frequency varies only slightly betweenrandom repeat-masked sequences and regions located immediatelyupstream of the known genes. Most of our study has been performedon the ENCODE sequences, which comprise about 1% of the humangenome.