ModuleOrganizer: Detecting modules in families of transposable elements

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Tempel, Sebastien ^a   Rousseau, Christine ^b   Tahi, Fariza ^a   Nicolas, Jacques ^c  

^a UNIVERSITY OF EVRY   (France)

^b UNIVERSITÉ DE TOULOUSE   (France)

^c CAMPUS DE BEAULIEU   (France)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX METHODS; DROSOPHILA MELANOGASTER; EUKARYOTIC GENOME; GENOME SEQUENCES; IN-DEPTH ANALYSIS; MULTIPLE ALIGNMENT; NUCLEOTIDE MUTATION; TRANSPOSABLE ELEMENTS;

BIOINFORMATICS;

GENES;

DROSOPHILA MELANOGASTER; EUKARYOTA;

ANIMAL; ARTICLE; COMPUTER PROGRAM; DROSOPHILA MELANOGASTER; GENETIC VARIABILITY; GENETICS; GENOME; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; TRANSPOSON;

ANIMALS; BASE SEQUENCE; DNA TRANSPOSABLE ELEMENTS; DROSOPHILA MELANOGASTER; GENETIC VARIATION; GENOME; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 77956798611     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-474     Document Type: Article

References (45)

1. Kidwell MG, Lisch DR. Perspective: transposable elements and host genome evolution. Trends Ecol Evol 2001, 15:95-99.
2. Craig NL, Craigie R, Gellert M, Lambowitz A. Mobile DNA II 2002, Washington DC: American Society for Microbiology Press.
3. Romanish MT, Nakamura H, Lai CB, Wang Y, L MD. A novel protein isoform of the multicopy human NAIP gene derives from intragenic Alu SINE promoters. PLoS One 2009, 4:e5761. 10.1371/journal.pone.0005761, 2685007, 19488400.
4. Cordaux R, Udit S, Batzer MA, Feschotte C. Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. Proc Natl Acad Sci USA 2006, 103:8101-6. 10.1073/pnas.0601161103, 1472436, 16672366.
5. Feschotte C, Pritham E J. DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet 2007, 41:331-68. 10.1146/annurev.genet.40.110405.090448, 2167627, 18076328.
6. Quesneville H, Nouaud D, Anxolabehere D. Recurrent recruitment of the THAP DNA-binding domain and molecular domestication of the P-transposable element. Mol Biol Evol 2005, 22:741-6. 10.1093/molbev/msi064, 15574804.
7. Almeida LM, Silva IT, Silva WAJ, Castro JP, Riggs PK, Carareto CM, E AM. The contribution of transposable elements to Bos taurus gene structure. Gene 2007, 390:180-9. 10.1016/j.gene.2006.10.012, 17157447.
8. Wessler SR, Bureau TE, White SE. LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Genet Dev 1995, 5:814-821.
9. Feschotte C, Mouches C. Evidence that a family of miniature inverted-repeat transposable elements (MITEs) from the Arabidopsis thaliana genome has arisen from a pogo-like DNA transposon. Mol Biol Evol 2000, 17:730-737.
10. Brudno M, Poliakov A, Minovitsky S, Ratnere I, Dubchak I. Multiple whole genome alignments and novel biomedical applications at the VISTA portal. Nucleic Acids Res 2007, 35:W669-W674. 10.1093/nar/gkm279, 1933192, 17488840.
11. Nix DA, Eisen MB. GATA: a graphic alignment tool for comparative sequence analysis. BMC Bioinformatics 2005, 6:9. 10.1186/1471-2105-6-9, 546196, 15655071.
12. Price AL, Jones NC, Pevzner PA. De novo identification of repeat families in large genomes. Bioinformatics 2005, (Suppl 1):i351-i358. 10.1093/bioinformatics/bti1018, 15961478.
13. Tempel S, Giraud M, Lavenier D, Lerman IC, Valin AS, Couée I, Amrani AE, Nicolas J. Domain organization within repeated DNA sequences: application to the study of a family of transposable elements. Bioinformatics 2006, 22:1948-54. 10.1093/bioinformatics/btl337, 16809391.
14. Potter SS. DNA sequence of a foldback transposable element in Drosophilia. Nature 1982, 297:201-204. 10.1038/297201a0, 6176872.
15. Smith M, Bringaud F, Papadopoulou B. Organization and evolution of two SIDER retroposon subfamilies and their impact on the Leishmania genome. BMC Genomics 2009, 10:240. 10.1186/1471-2164-10-240, 2689281, 19463167.
16. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogentic and Genome Research 2005, 110:462-467.
17. Ukkonen E. On-line construction of suffix-trees. Algorithmica 1995, 14:249-260.
18. Bieganski P, Riedl J, Carlis J, Retzel E. Generalized Suffix Trees for Biological Sequence Data. Biotechnology Computing, Proceedings of the Twenty-Seventh Hawaii International Conference 1994, 35-44.
19. Gusfield D. Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology 1997, Cambridge University Press, ISBN 0-521-58519-8.
20. Choi KH, Kim KJ. Applications of transposon-based gene delivery system in bacteria. J Microbiol Biotechnol 2009, 19:217-28.
21. Parks AR, Peters JE. Tn7 elements: engendering diversity from chromosomes to episomes. Plasmid 2009, 61:1-14. 10.1016/j.plasmid.2008.09.008, 2614081, 18951916.
22. Kapitonov V, Jurka J. Helitrons on a roll: eukaryotic rolling-circle transposons. Trends Genet 2007, 23:521-9. 10.1016/j.tig.2007.08.004, 17850916.
23. Hanada K, Vallejo V, Nobuta K, Slotkin RK, Lisch D, Meyers BC, Shiu SH, Jiang N. The functional role of pack-MULEs in rice inferred from purifying selection and expression profile. Plant Cell 2009, 21:25-38. 10.1105/tpc.108.063206, 2648092, 19136648.
24. Yang L, Bennetzen JL. Distribution, diversity, evolution, and survival of Helitrons in the maize genome. Proc Natl Acad Sci USA 2009, 106:19922-7. 2785268, 19926865.
25. Yang G, Zhang F, Hancock CN, R WS. Transposition of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana. Proc Natl Acad Sci USA 2007, 104:10962-10967. 10.1073/pnas.0702080104, 1904124, 17578919.
26. Yang G, Nagel DH, Feschotte C, N HC, Wessler SR. Tuned for transposition: molecular determinants underlying the hyperactivity of a Stowaway MITE. Science 2009, 325:1391-4. 10.1126/science.1175688, 19745152.
27. Casals F, Cáceres M, Maanfrin MH, Gonázales J, Ruiz A. Molecular characterization and chromosomal distribution of Galileo, Kepler and Newton, three folback transposable element in Drosophila buzzati species complex. Genetics 2005, 169:2047-2059. 10.1534/genetics.104.035048, 1449584, 15695364.
28. Windsor AJ, Wadell CS. FARE, a new family of foldback transposons in Arabidopsis. Genetics 2000, 156:1983-1995. 1461375, 11102389.
29. Dooner HK, Weil CF. Give-and-take: interactions between DNA transposons and their host plant genomes. Curr Opin Genet Dev 2007, 17:486-92. 10.1016/j.gde.2007.08.010, 17919898.
30. Marsan L, Sagot MF. Algorithms for Extracting Structured Motifs Using a Suffix Tree with an Application to Promoter and Regulatory Site Consensus Identification. Journal of Computational Biology 2000, 7(3-4):345-362. 10.1089/106652700750050826, 11108467.
31. Altschul SF, Madden TL, Schaeffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
32. Ivics Z, Kaufman CD, Zayed H, Miskey C, Walisko O, Izsvá ZK. The Sleeping Beauty Transposable Element: Evolution, Regulation and Genetic Applications. Curr Issues Mol Biol 2004, 6:43-56.
33. Bigot Y, Brillet B, Augé-Gouillou C. Conservation of Palindromic and Mirror Motifs within Inverted Terminal Repeats of mariner-like Elements. J Mol Biol 2005, 351:108-16. 10.1016/j.jmb.2005.05.006, 15946679.
34. Ward JH. Hierarchical Grouping to Optimize an Objective Function. Journal of the American Statistical Association 1963, 58:236-244.
35. Nicolas J, Durand P, Ranchy G, Tempel S, Valin AS. Suffix-tree analyser (STAN): looking for nucleotidic and peptidic patterns in chromosomes. Bioinformatics 2005, 21:4408-4410. 10.1093/bioinformatics/bti710, 16223791.
36. FGENESH software. , http://www.softberry.com/berry.phtml
37. Bao Z, Eddy SR. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res 2002, 12:1269-1276. 10.1101/gr.88502, 186642, 12176934.
38. Helden J, Rios AF, Collado-Vides J. Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucl Acids Res 2000, 28(8):1808-1818. 10.1093/nar/28.8.1808, 102821, 10734201.
39. Pisanti N, Carvalho A, Marsan L, Sagot MF. RISOTTO: Fast Extraction of Motifs with Mismatches. LATIN, Lecture Notes in Computer Science 2006, 3887:757-768. Springer, Correa JR, Hevia A, Kiwi MA.
40. Mehldau G, Myers G. A system for pattern matching applications on biosequences. Computer Applications in the Biosciences (Bioinformatics) 1993, 9(3):299-314.
41. Morgante M, Policriti A, Vitacolonna N, Zuccolo A. Structured Motifs Search. Journal of Computational Biology 2005, 12(8):1065-1082. 10.1089/cmb.2005.12.1065, 16241898.
42. Zhang Y, Zaki M. SMOTIF: efficient structured pattern and profile motif search. Algorithms for Molecular Biology 2006, 1:22. 10.1186/1748-7188-1-22, 1679804, 17118189.
43. Halachev M, Shiri N. Fast Structured Motif Search in DNA Sequences. Bioinformatics Research and Development, 2nd Int. Conference, BIRD 2008, Vienna, Austria, July 7-9, 2008 2008, 13:58-73. Communications in Computer and Information Science, Springer.
44. Thomas JM, Horspool D, Brown B, Tcherepanov V, Upton C. GraphDNA: a Java program for graphical display of DNA composition analyses. BMC Bioinformatics 2007, 8:21. 10.1186/1471-2105-8-21, 1783863, 17244370.
45. Tatusova TA, Madden TL. BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 1999, 174:247-250. 10.1111/j.1574-6968.1999.tb13575.x, 10339815.