Improved repeat identification and masking in Dipterans

Gene

Volumn 389, Issue 1, 2007, Pages 1-9

  Smith, Christopher D ^a,b   Edgar, Robert C ^c   Yandell, Mark D ^d   Smith, Douglas R ^e   Celniker, Susan E ^b   Myers, Eugene W ^f,g   Karpen, Gary H ^a,b  

^a SAN FRANCISCO STATE UNIVERSITY   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c University of Utah ^*

^d UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

^g HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

A. gambiae; Drosophila; Heterochromatin; PILER; RepeatRunner; Transposable element

Indexed keywords

ARTICLE; CHROMOSOME; COMPUTER PROGRAM; CONTROLLED STUDY; FLY; GENE CONTROL; GENE IDENTIFICATION; GENOMIC INSTABILITY; LABORATORY TEST; MICROARRAY ANALYSIS; NONHUMAN; PRIORITY JOURNAL;

ANIMALS; DIPTERA; DNA TRANSPOSABLE ELEMENTS; EUCHROMATIN; GENOME, INSECT; HETEROCHROMATIN; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; SOFTWARE; SPECIES SPECIFICITY; TANDEM REPEAT SEQUENCES;

DIPTERA; EUKARYOTA;

EID: 33846224659     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2006.09.011     Document Type: Article

References (49)

1. AAA. Assembly, Alignment, and Annotation of Drosophilid Genomes (2006). http://rana.lbl.gov/drosophila/caf1.html. http://rana.lbl.gov/drosophila/caf1.html
2. Agencourt B. The Genomes of D. mojavensis, D. ananassae (2005). http://www.agencourt.com/ http://www.agencourt.com/
3. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
4. Ashburner M. The Natural Transposable Element Project (2005). http://www.bdgp.org/p_disrupt/TE.html. http://www.bdgp.org/p_disrupt/TE.html
5. Aultman K.S., Gottlieb M., Giovanni M.Y., and Fauci A.S. Anopheles gambiae genome: completing the malaria triad. Science 298 (2002) 13
6. BDGP. Berkeley Drosophila Genome Project (2006). http://www.bdgp.org. http://www.bdgp.org
7. Bejerano G., et al. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 441 (2006) 87-90
8. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27 (1999) 573-580
9. Bernstein E., and Allis C.D. RNA meets chromatin. Genes Dev. 19 (2005) 1635-1655
10. Britten R. Transposable elements have contributed to thousands of human proteins. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 1798-1803
11. Broad Institute. The Genomes of D. sechellia ad D. persimilis (2006). http://www.broad.mit.edu/ http://www.broad.mit.edu/
12. Burge C., and Karlin S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268 (1997) 78-94
13. Carlson J., et al. The Release 5 Genome Sequence of D. melanogaster (2006)
14. Casacuberta E., and Pardue M.L. RNA interference has a role in regulating Drosophila telomeres. Genome Biol. 7 (2006) 220
15. Casacuberta E., Casacuberta J.M., Puigdomenech P., and Monfort A. Presence of miniature inverted-repeat transposable elements (MITEs) in the genome of Arabidopsis thaliana: characterisation of the Emigrant family of elements. Plant J. 16 (1998) 79-85
16. Caspi A., and Pachter L. Identification of transposable elements using multiple alignments of related genomes. Genome Res. 16 (2006) 260-270
17. Celniker S.E., and Rubin G.M. The Drosophila melanogaster genome. Annu. Rev. Genomics Hum. Genet. 4 (2003) 89-117
18. Deininger P.L., Moran J.V., Batzer M.A., and Kazazian Jr. H.H. Mobile elements and mammalian genome evolution. Curr. Opin. Genet. Dev. 13 (2003) 651-658
19. Edgar R.C., and Myers E.W. PILER: identification and classification of genomic repeats. Bioinformatics 21 Suppl 1 (2005) i152-i158
20. Engels W.R. The P family of transposable elements in Drosophila. Annu. Rev. Genet. 17 (1983) 315-344
21. GNU-Project. R - an Open Source Environment for Graphing and Statistics (2006). http://www.r-project.org/. http://www.r-project.org/
22. Grady D.L., Ratliff R.L., Robinson D.L., McCanlies E.C., Meyne J., and Moyzis R.K. Highly conserved repetitive DNA sequences are present at human centromeres. Proc. Natl. Acad. Sci. U. S. A. 89 (1992) 1695-1699
23. Hansen R.S. X inactivation-specific methylation of LINE-1 elements by DNMT3B: implications for the Lyon repeat hypothesis. Hum. Mol. Genet. 12 (2003) 2559-2567
24. Hikosaka A., Yokouchi E., and Kawahara A. Extensive amplification and transposition of a novel repetitive element, xstir, together with its terminal inverted repeat in the evolution of Xenopus. J. Mol. Evol. 51 (2000) 554-564
25. Hoskins R.A., et al. Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biol. 3 (2002) (RESEARCH0085)
26. Jurka J., Kapitonov V.V., Pavlicek A., Klonowski P., Kohany O., and Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110 (2005) 462-467
27. Kaminker J.S., et al. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol. 3 (2002) (RESEARCH0085)
28. Kapitonov V.V., and Jurka J. Rolling-circle transposons in eukaryotes. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 8714-8719
29. Kazazian Jr. H.H. Mobile elements: drivers of genome evolution. Science 303 (2004) 1626-1632
30. Lander E.S., et al. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
31. Misra S., et al. Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biol. 3 (2002) (RESEARCH0083)
32. Price A.L., Eskin E., and Pevzner P.A. Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. Genome Res. 14 (2004) 2245-2252
33. Quesneville H., et al. Combined evidence annotation of transposable elements in genome sequences. PLoS Comput. Biol. 1 (2005) 166-175
34. Reese M.G., Eeckman F.H., Kulp D., and Haussler D. Improved splice site detection in Genie. J. Comput. Biol. 4 (1997) 311-323
35. Richards S., et al. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res. 15 (2005) 1-18
36. Roberts J.D., Preston B.D., Johnston L.A., Soni A., Loeb L.A., and Kunkel T.A. Fidelity of two retroviral reverse transcriptases during DNA-dependent DNA synthesis in vitro. Mol. Cell Biol. 9 (1989) 469-476
37. Smit A., Hubley R., and Green P. RepeatMasker Open-3.0 (1996-2004). http://www.repeatmasker.org. http://www.repeatmasker.org
38. Smit A., Hubley R., and Green P. RepeatMasker Open-3.0 (2005). http://www.repeatmasker.org/cgi-bin/RepeatProteinMaskRequest http://www.repeatmasker.org/cgi-bin/RepeatProteinMaskRequest
39. Sorek R., Ast G., and Graur D. Alu-containing exons are alternatively spliced. Genome Res. 12 (2002) 1060-1067
40. Sorek R., et al. Minimal conditions for exonization of intronic sequences: 5′ splice site formation in alu exons. Mol. Cell 14 (2004) 221-231
41. Spradling A.C., et al. The Berkeley Drosophila Genome Project gene disruption project: single P-element insertions mutating 25% of vital Drosophila genes. Genetics 153 (1999) 135-177
42. Thornburg B.G., Gotea V., and Makalowski W. Transposable elements as a significant source of transcription regulating signals. Gene 365 (2006) 104-110
43. TIGR. Genome Sequence of D. willistoni (2005). http://www.tigr.org. http://www.tigr.org
44. Tu Z. Three novel families of miniature inverted-repeat transposable elements are associated with genes of the yellow fever mosquito, Aedes aegypti. Proc. Natl. Acad. Sci. U. S. A. 94 (1997) 7475-7480
45. Tu Z. Eight novel families of miniature inverted repeat transposable elements in the African malaria mosquito, Anopheles gambiae. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 1699-1704
46. Waterston R.H., et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420 (2002) 520-562
47. WUSTL. Genome Sequence of D. yakuba and D. simulans (2005). http://genome.wustl.edu/. http://genome.wustl.edu/
48. Yandell M. Comparative Genomics Library - RepeatRunner (2006). http://www.yandell-lab.org/repeat_runner/index.html. http://www.yandell-lab.org/repeat_runner/index.html
49. Yandell M., et al. Large-scale trends in the evolution of gene structures within 11 animal genomes. PLoS Comput. Biol. 2 (2006) e15