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Functional & Integrative Genomics

, Volume 7, Issue 3, pp 221–227 | Cite as

The human genome-wide distribution of DNA palindromes

  • Le Lu
  • Hui Jia
  • Peter Dröge
  • Jinming LiEmail author
Original Paper

Abstract

In this work, we performed a systematic study of perfect and nonspacer palindromes present in human genomic DNA, and we investigated palindrome distribution over the entire human genome and over the functional regions such as the exon, intron, intergenic, and upstream regions (2,000 bp upstream from translational start site). We found that 24 palindrome-abundant intervals are mostly located on G-bands, which condense early, replicate late, and are relatively A+T rich. In general, palindromes are overrepresented in introns but underrepresented in exons. Upstream region has enriched palindrome distribution, where palindromes can serve as transcription factor binding sites. We created a Human DNA Palindrome Database (HPALDB) which is accessible at http://vhp.ntu.edu.sg/hpaldb. It contains 12,556,994 entries covering all palindromes in the human genome longer than 6 bp. Queries can be performed in different ways. Each entry in the database is linked to its location on NCBI’s human chromosome Map Viewer.

Keywords

Palindrome Genomic distribution 

Notes

Acknowledgments

We acknowledge the financial support of Nanyang Technological University, Singapore. We are particularly grateful to the two anonymous reviewers for their constructive comments and suggestions that significantly improved the presentation of the manuscript.

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Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  1. 1.Division of Structural and Computational Biology, School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
  2. 2.Division of Genomics and Genetics, School of Biological SciencesNanyang Technological UniversitySingaporeSingapore

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