LTrsift: A graphical user interface for semiautomatic classification and postprocessing of de novo detected LTR retrotransposons

Mobile DNA

Volumn 3, Issue 1, 2012, Pages

  Steinbiss, Sascha ^a   Kastens, Sascha ^a   Kurtz, Stefan ^a  

^a UNIVERSITY OF HAMBURG   (Germany)

Author keywords

Annotation; Classification; ERV; LTR retrotransposons; Postprocessing; Prediction; Software; User interface

Indexed keywords

EID: 84990838249     PISSN: None     EISSN: 17598753     Source Type: Journal    
DOI: 10.1186/1759-8753-3-18     Document Type: Article

References (54)

1. International Human Genome Sequencing Consortium: Initial sequencing and analysis of the human genome. Nature 2001, 409(6822):860–921.
2. Mouse Genome Sequencing Consortium: Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520–562.
3. Finnegan DJ: Eukaryotic transposable elements and genome evolution. Trends Genet 1989, 5:103–107.
4. Wicker T, Sabot F, Hua-Van A, Bennetzen J, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman A: A unified classification system for eukaryotic transposable elements. Nat Rev Genet 2007, 8(12):973–982. [http://dx.doi.org/10.1038/nrg2165]
5. Steinbiss S, Willhoeft U, Gremme G, Kurtz S: Fine-grained annotation and classification of de novo predicted LTR retrotransposons. Nucleic Acids Res. 2009, 37:7002–7013. [http://nar.oxfordjournals.org/cgi/content/full/37/21/7002]
6. Marquet R, Isel C, Ehresmann C, Ehresmann B: tRNAs as primer of reverse transcriptases. Biochimie 1995, 77:113–124.
7. Mak J, Kleiman L: Primer tRNAs for reverse transcription. J Virol 1997, 71:8087–8095.
8. Wilhelm M, Wilhelm FX: Reverse transcription of retroviruses and LTR retrotransposons. Cell Mol Life Sci 2001, 58:1246–1262.
9. Wilhelm M, Heyman T, Boutabout M, Wilhelm FX: A sequence immediately upstream of the plus-strand primer is essential for plus-strand DNA synthesis of the Saccharomyces cerevisiae Ty1 retrotransposon. Nucleic Acids Res 1999, 27:4547–4552.
10. Bergman CM, Quesneville H: Discovering and detecting transposable elements in genome sequences. Brief Bioinform 2007, 8:382–392.
11. McCarthy EM, McDonald JF: LTR STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 2003, 19:362–367.
12. Rho M, Choi JH, Kim S, Lynch M, Tang H: De novo identification of LTR retrotransposons in eukaryotic genomes. BMC Genomics 2007, 8:90.
13. Xu Z, Wang H: LTR FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res 2007, 35:W265–W268.
14. Ellinghaus D, Kurtz S, Willhoeft U: LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics 2008, 9:18. [http://www.biomedcentral.com/1471-2105/9/ 18]
15. Minervini CF, Viggiano L, Caizzi R, Marsano RM: Identification of novel LTR retrotransposons in the genome of Aedes aegypti. Gene 2009, 440(1–2):42–49. [http://www.sciencedirect.com/science/article/pii/ S0378111909001590]
16. Marsano RM, Leronni D, D’Addabbo P, Viggiano L, Tarasco E, Caizzi R: Mosquitoes LTR retrotransposons: a deeper view into the genomic sequence of Culex quinquefasciatus. PLoS ONE 2012, 7:e30770. [http://dx.doi.org/10.13712Fjournal.pone.0030770]
17. Rho M, Schaack S, Gao X, Kim S, Lynch M, Tang H: LTR retroelements in the genome of Daphnia pulex. BMC Genomics 2010, 11:425. [http://www.biomedcentral.com/1471- 2164/11/425]
18. McCarthy EM, McDonald JF: Long terminal repeat retrotransposons of Mus musculus. Genome Biol 2004, 5:R14.
19. Polavarapu N, Bowen NJ, McDonald JF: Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses. Genome Biol 2006, 7:R51. [http://genomebiology.com/2006/7/6/R51]
20. Huda A, Polavarapu N, Jordan IK, McDonald JF: Endogenous retroviruses of the chicken genome. BiolDirect 2008, 3:9. [http://www.biology-direct.com/content/3/1/9]
21. de la Chaux N, Wagner A: BEL/Pao retrotransposons in metazoan genomes. BMC Evolutionary Biol 2011, 11:154. [http://www.biomedcentral.com/1471- 2148/11/154]
22. McCarthy E, Liu J, Lizhi G, McDonald JF: Long terminal repeat retrotransposons of Oryza sativa. Genome Biol 2002, 3(10):research0053.1–research0053.11. [http://genomebiology.com/2002/3/10/research/0053]
23. Wang H, Liu JS: LTR retrotransposon landscape in Medicago truncatula: more rapid removal than in rice. BMC Genomics 2008, 9:382. [http://www.biomedcentral.com/1471- 2164/9/382]
24. Seberg O, Petersen G: A unified classification system for eukaryotic transposable elements should reflect their phylogeny. NatRevGenet 2009, 10(4):276. [http://dx.doi.org/10.1038/nrg2165-c3]
25. Kapitonov VV, Jurka J: A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet 2008, 9:411–412. [http://dx.doi.org/10.1038/nrg2165- c1]
26. Abrusán G, Grundmann N, DeMester L, Makalowski W: TEclass – a tool for automated classification of unknown eukaryotic transposable elements. Bioinformatics 2009, 25(10):1329–1330.
27. Feschotte C, Keswani U, Ranganathan N, Guibotsy ML, Levine D: Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable Elements in eukaryotic genomes. Genome Biol Evol 2009, 2009:205–220.
28. Kapitonov VV, Tempel S, Jurka J: Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences. Gene 2009, 448(2):207–213. [http://www.biomedsearch.com/nih/Simple-fast-classification-non-LTR/19651192. html]
29. Rouault JD, Casse N, Chénais B, Hua-Van A, Filée J, Capy P: Automatic classification within families of transposable elements: Application to the mariner family. Gene 2009, 448(2):227–232. [http://www.sciencedirect.com/science/article/pii/S0378111909004570]
30. The Vmatch large scale sequence analysis software. [http://www.vmatch.de]
31. Tempel S, Rousseau C, Tahi F, Nicolas J: ModuleOrganizer: detecting modules in families of transposable elements. BMCBioinformatics 2010, 11:474. [http://www.biomedcentral.com/1471-2105/11/474]
32. Smit AFA, Hubley R, Green P: RepeatMasker Open-3.0. Unknown Month 1996. [http://www.repeatmasker.org]
33. Stein L: Generic Feature Format Version 3. [http://www.sequenceontology.org/gff3.shtml]
34. Steinbiss S, Kurtz S: A new efficient data structure for storage and retrieval of multiple biosequences. IEEE/ACM Trans Comput Biol Bioinform 2012, 9(2):345–357. [http://www.computer.org/portal/web/ csdl/doi/10.1109/TCBB.2011.146]
35. Eilbeck K, Lewis S, Mungall C, Yandell M, Stein L, Durbin R, Ashburner M: The sequence ontology: a tool for the unification of genome annotations. Genome Biol 2005, 6(5):R44. [http://genomebiology.com/2005/6/5/R44]
36. Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC: Adaptive seeds tame genomic sequence comparison. Genome Res 2011, 21(3):487–493. [http://genome.cshlp.org/content/early/2011/02/04/gr.113985.110. abstract]
37. Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri AK, Keefe D, Keenan S, Kinsella R, Komorowska M, Koscielny G, Kulesha E, Larsson P, Longden I, McLaren W, Muffato M, Overduin B, Pignatelli M, Pritchard B, Riat HS, et al.: Ensembl 2012. Nucleic Acids Res 2012, 40(D1):D84–D90. [http://nar.oxfordjournals.org/content/40/D1/D84.abstract]
38. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403–410.
39. Ierusalimschy R, de Figueiredo LH, Filho WC: Lua – an extensible extension language. Software: Practice & Experience 1996, 26:635–652.
40. Krause A: Foundations of GTK+ Development. Berkeley, CA, USA: Apress; 2007.
41. The GTK+ Project. [http://www.gtk.org]
42. GIMP – The GNU Image Manipulation Program. [http://www.gimp. org]
43. GNOME. [http://www.gnome.org]
44. Gremme G, Steinbiss S, Kurtz S: GenomeTools. [http://genometools.org]
45. Steinbiss S, Gremme G, Schärfer C, Mader M, Kurtz S: AnnotationSketch: a genome annotation drawing library. Bioinformatics 2009, 25(4):533–534. [http://bioinformatics.oxfordjournals.org/cgi/content/full/25/4/533]
46. Worth C, Packard K: Xr: Cross-device rendering for vector graphics. In Proceedings of the Ottawa Linux Symposium; 2003. [http://cworth.org/cworth/papers/xr ols2003]
47. Fink. [http://www.finkproject.org]
48. Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SMJ, Sharpe T, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, et al.: Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 2007, 447(7141):167–177. [http://www.nature.com/nature/journal/v447/n7141/full/nature05805.html]
49. Samollow PB: The opossum genome: Insights and opportunities from an alternative mammal. Genome Res 2008, 18(8):1199–1215. [http://genome.cshlp.org/content/18/8/1199.abstract]
50. Gentles AJ, Wakefield MJ, Kohany O, Gu W, Batzer MA, Pollock DD, Jurka J: Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. Genome Res 2007, 17(7):992–1004. [http://genome.cshlp.org/content/17/7/992.abstract]
51. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J: Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 2005, 110:462–467.
52. Ensembl genome browser 67: Monodelphis domestica. [http://www.ensembl.org/Monodelphis domestica/Info/Index]
53. Tempel S, Jurka M, Jurka J: VisualRepbase: an interface for the study of occurrences of transposable element families. BMCBioinformatics 2008, 9:345. [http://dx.doi.org/10.1186/1471-2105-9-345]
54. Larkin M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H, Valentin F, Wallace I, Wilm A, Lopez R, Thompson J, Gibson T, Higgins D: Clustal W and Clustal X version 2.0.. Bioinformatics 2007, 23(21):2947–2948.