Are the Available DNA Sequence Alignments and Search Tools Reliable for Alu Research?
AbstractThe results of most bioinformatics and microbiology research studies that use SINEs depend entirely on the mechanism used to detect and count these element instances in the genome. Hence, the reliability and accuracy of the DNA sequence alignment and search tool is vital for genetic researches. This research report presents the findings from testing the reliability of some popular DNA Sequence alignment and search (SA&S) tools using a test/known genomic sequence. The findings reveal the need for novel tool design.
A.M. Shedlock, K. Takahashi and N. Okada, "SINEs of speciation: tracking lineages with retroposons", Trends in Ecology and Evolution, vol.19 (10), October 2004, pp. 545 - 553.
A.L. Price, E. Eskin, and P.A. Pevzner, “Whole-genome analysis of Alu repeat elements reveals complex evolutionary history”, Genome Re-search, vol. 14, November 2004, pp. 2245 – 2252.
A.M. Roy-Engel, M.L. Carroll, M. El-Sawy, A.H. Salem, R.K. Garber, S.V. Nguyen, P.L. Deininger, M.A. Batzer, “ Non- traditional Alu evolution and primate genomic diversity”, J. Mol. Biol., vol. 316, no. 5, March 8, 2002, pp. 1033 – 1040.
A-H. Salem, G. E. Kilroy, W. S. Watkins, L. B. Jorde, and M. A. Batzer, "Recently Integrated Alu Elements and Human Genomic Diversity", Molecular Biology. Evolution, vol. 20(8), pp. 1349–1361, 2003.
D. Comas, S. Plaza, F. Calafell, A. Sajantila and J. Bertranpetit, “Recent Insertion of an Alu Element within a Polymorphic Human-Specific Alu Insertion,” Molecular Biology and Evolution, vol. 18, pp. 85-88, 2001.
D. Grover, P.P. Majumder, C.B. Rao, S.K. Brahmachari, and M. Mukerji, “Nonrandom Distribution of Alu Elements in Genes of Various Functional Categories: Insight from Analysis of Human Chromosomes 21 and 22”, Molecular Biology and Evolution, vol. 20(9), pp. 1420 – 1424, 2003.
D.J. Hedges, P.A. Callinan, R. Cordaux, J. Xing, E. Barnes, and M.A. Batzer, “ Differential Alu Mobilization and Polymorphism Among the Human and Chimpanzee Lineages”, Genome Research, vol. 14, 2004, pp. 1068 – 1075.
G. S. Attard, A. C. Hurworth and J. P. Jack, "Language-like features in DNA: transposable element foot-prints in the genome", Europhys. Lett, 36 (5), 1996, pp. 391-396.
J. Brosius, "How significant is 98.5% ‘junk’ in mammalian genomes?", Bioinformatics, vol. 19, Suppl. 2, 2003, pp. ii35.
J. Gephart, “Tracing Human Origins with “Alu” Markers”, http://www. pnl.gov/er_news/10 _95/ er_news/XALU-MARK.JG.html, March 20, 2006.
J. Whitfield, “How the sequence got the way it is”, email@example.com, http://news .nature .com//-news/2001 /010215/010215-1.html, February 12, 2001.
K. Han, J. Xing, H. Wang, D.J. Hedges, R. K. Garber, R. Cordaux, and M.A. Batzer, "Under the genomic radar: The Stealth model of Alu amplification", Genome Research, vol.5 , 2005, pp. 655 – 664.
M. El-Sawy, and P. Deininger, “Tandem insertions of Alu elements”, Cytogenetic and Genome Research, vol. 108, pp. 58 – 62, 2005.
P.L. Deininger, and M.A. Batzer, “Mammalian Retroelements”, Genome Research, vol. 12, 2002, pp. 1455 – 1465.
W. Makalowski, “Not Junk After All”, Science, vol. 300, May 23, 2003, pp. 1246 – 1247.
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