De novo identification of LTR retrotransposons in eukaryotic genomes

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Rho, Mina ^a   Choi, Jeong Hyeon ^a   Kim, Sun ^a,b   Lynch, Michael ^a   Tang, Haixu ^a,b  

^a INDIANA UNIVERSITY   (United States)

^b INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; CAENORHABDITIS BRIGGSAE; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; DROSOPHILA PSEUDOOBSCURA; EUKARYOTE; GENOME; LONG TERMINAL REPEAT; NONHUMAN; PROBABILITY; PROTEIN ANALYSIS; PROTEIN DOMAIN; RETROPOSON; SENSITIVITY ANALYSIS; AMINO ACID SEQUENCE; ANIMAL; CHROMOSOME MAP; CLUSTER ANALYSIS; COMPARATIVE STUDY; COMPUTER PROGRAM; DNA SEQUENCE; DROSOPHILA; EUKARYOTIC CELL; EVALUATION; GENETICS; METHODOLOGY; MOLECULAR GENETICS; PHYLOGENY; SEQUENCE HOMOLOGY;

CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; EUKARYOTA;

AMINO ACID SEQUENCE; ANIMALS; CAENORHABDITIS ELEGANS; CHROMOSOME MAPPING; CLUSTER ANALYSIS; DROSOPHILA; EUKARYOTIC CELLS; GENOME; MOLECULAR SEQUENCE DATA; PHYLOGENY; RETROELEMENTS; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE; TERMINAL REPEAT SEQUENCES;

EID: 34247877564     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-90     Document Type: Article

References (41)

1. Kidwell MG Lisch D Transposable elements as sources of variation in animals and plants. Proc Natl Acad Sci U S A 1997 94 15 7704-7711 33680 9223252 10.1073/pnas.94.15.7704
2. Brookfield JF The ecology of the genome - mobile DNA elements and their hosts. Nat Rev Genet 2005 6 128-136 10.1038/nrg1524 15640810
3. Jurka J Repbase update: A database and an electronic journal of repetitive elements. Trends Genet 2000 16 9 418-420 10.1016/ S0168-9525(00)02093-X 10973072
4. Smit A RepeatMasker http://www.genome.washington.edu/uwgc/analysistools/ repeatmask.htm unpublished
5. Holmes I Transcendent elements: Whole-genome transposon screens and open evolutionary questions. Genome Res 2002 12 8 1152-1155 10.1101/gr.453102 12176921
6. Bao Z Eddy SR Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res 2002 12 8 1269-1276 186642 12176934 10.1101/gr.88502
7. Price AL Jones NC Pevzner PA De novo identification of repeat families in large genomes. Bioinformatics 2005 21 Suppl 1 i351-.i358 10.1093/ bioinformatics/bti1018 15961478
8. Edgar RC Myers EW PILER: Identification and classification of genomic repeats. Bioinformatics 2005 21 Suppl 1 i152-i158 10.1093/bioinformatics/ bti1003 15961452
9. Quesneville H Bergman CM Andrieu O Autard D Nouaud D Ashburner M Anxolabehere D Combined evidence annotation of transposable elements in genome sequences. PLoS Comput Biol 2005 1 2 166-175 1185648 16110336 10.1371/journal.pcbi.0010022
10. Bailey JA Eichler EE Genome-wide detection and analysis of recent segmental duplications within mammalian organisms. Cold Spring Harb Symp Quant Biol 2003 68 115-124 10.1101/sqb.2003.68.115 15338609
11. Jiang N Bao Z Zhang X Hirochika H Eddy SR McCouch SR Wessler SR An active DNA transposon family in rice. Nature 2003 421 6919 163-167 10.1038/nature01214 12520302
12. Caspi A Pachter L Identification of transposable elements using multiple alignments of related genomes Genome Research 2006 16 260-270
13. SanMiguel P Gaut BS Tikhonov A Nakajima Y Bennetzen JL The paleontology of intergene retrotransposons of maize. Nat Genet 1998 20 43-45 9731528
14. Ganko EW Fielman KT McDonald JF Evolutionary History of Cer Elements and Their Impact on the C. elegans Genome Genome Research 2001 11 2066-2074 10.1101/gr.196201
15. Kaminker JS Bergman CM Kronmiller B Carlson J Svirskas R Patel S Frise E Wheeler DA Lewis SE Rubin GM Ashburner M Celniker SE The transposable elements of the Drosophila melanogaster euchromatin: A genomics perspective Genome Biology 2002 3 research0084.1-0084.20 10.1186/ gb-2002-3-12-research0084
16. Lerat E Rizzon C Biémont C Sequence Divergence Within Transposable Element Families in the Drosophila melanogaster Genome Genome Research 2003 13 1889-1896
17. McCarthy EM McDonald JF Long terminal repeat retrotransposons of Mus musculus. Genome Biol 2004 5 3 R14 395764 15003117 10.1186/ gb-2004-5-3-r14
18. Ma J Devos KM Bennetzen JL Analyses of LTR-Retrotransposon Structures Reveal Recent and Rapid Genomic DNA Loss in Rice Genome Research 2004 14 860-869 10.1101/gr.1466204
19. McCarthy EM McDonald JF LTR_STRUC: A novel search and identification program for LTR retrotransposons. Bioinformatics 2003 19 3 362-367 10.1093/bioinformatics/btf878 12584121
20. Kalyanaraman A Aluru S Efficient algorithms and software for detection of full-length LTR retrotransposons J Bioinform Comput Biol 2006 4 2 197-216 10.1142/S021972000600203X 16819780
21. Havecker ER Gao X Voytas DF The diversity of LTR retrotransposons. Genome Biol 2004 5 6 225 463057 15186483 10.1186/gb-2004-5-6-225
22. Kim S Lee J A Graph Theoretic Sequence Clustering Algorithm Int J Data Mining Bioinformatics 2006 1 2 178-200 10.1504/IJDMB.2006.010855
23. http://genome.ucsc.edu
24. Kalyanaraman A Aluru S Efficient Algorithms and Software for Detection of Fell-Length LTR Retrotransposons: Stanford University. World Scientific press Markstein P, Xu Y 2005
25. Stein LD Bao Z Blasiar D Blumenthal T Brent MR Chen N Chinwalla A Clarke L Clee C Coghlan A Coulson A D'Eustachio P Fitch DH Fulton LA Fulton RE Griffiths-Jones S Harris TW Hillier LW Kamath R Kuwabara PE Mardis ER Marra MA Miner TL Minx P Mullikin JC Plumb RW Rogers J Schein JE Sohrmann M Spieth J Stajich JE Wei C Willey D Wilson RK Durbin R Waterston RH The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics. PLoS Biol 2003 1 2 E45 261899 14624247 10.1371/ journal.pbio.0000045
26. Bowen NJ McDonald JF Drosophila Euchromatic LTR Retrotransposons are Much Younger Than the Host Species in Which They Reside Genome Research 2001 11 1527-1540 311128 11544196 10.1101/gr.164201
27. Kapitonov VV Jurka J Molecular paleontology of transposable elements in the Drosophila melanogaster genome Proc Natl Acad Sci USA 2003 100 6569-6574 10.1073/pnas.0732024100
28. Rizzon C Marais G Gouy M Biémont C Recombination Rate and the Distribution of Transposable Elements in the Drosophila melanogaster Genome Genome Research 2002 12 400-407 10.1101/gr.210802. Article published online before print in February 2002
29. Vieira C Lepetit D Dumont S Biémont C Wake Up of Transposable Elements Following Drosophila simulans Worldwide Colonization Mol Biol Evol 1999 16 1251-1255
30. Riddle DL Blumenthal T Meyse BJ Priess JR C. elegans II Cold Spring Harbor Laboratory Press 1997
31. ftp://ftp.sanger.ac.uk/pub/wormbase
32. http://www.fruitfly.org/sequence/release4genomic.shtml
33. Flybase ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Dpseudoobscura
34. Kasai T Lee G Arimura H Arikawa S Park K Linear-time longest common-prefix computation in suffix arrays and its applications.: Jerusalem, Israel. Springer-Verlag Lecture Notes in Computer Science 2002 2089 181-192
35. Choi JH Cho HG Kim S Alignment method for microbial whole Genomes using maximal exact match filtering Computational Biology and Chemistry 2005 29 3 244-253 10.1016/j.compbiolchem.2005.04.004
36. Manber U Myers G Suffix arrays: A new method for on-line string searches SIAM J Comput 1993 22 5 935-948 10.1137/0222058
37. Bateman A Coin L Durbin R Finn RD Hollich V Griffiths-Jones S Khanna A Marshall M Moxon S Sonnhammer EL Studholme DJ Yeats C Eddy SR The Pfam protein families database. Nucleic Acids Res 2004 32 Database issue D138-D141 308855 14681378 10.1093/nar/gkh121
38. HMMer http://hmmer.wustl.edu
39. http://darwin.informatics.indiana.edu/cgi-bin/evolution/ltr.pl
40. Ramu C Sugawara H Koike T Lopez R Gibson TJ Higgins DG Thompson JD Multiple sequence alignment with the Clustal series of programs Nucleic Acids Res 2003 31 13 3497-3500 168907 12824352 10.1093/nar/gkg546
41. Felsenstein J PHYLIP - Phylogeny Inference Package (Version 3.2) Cladistics 1989 5 164-166