-
1
-
-
36549068275
-
Computational analysis and paleogenomics of interspersed repeats in eukaryotes
-
Stojanovic,N. (ed). Taylor & Francis, London
-
Feschotte,C. and Pritham,E.J. (2007) Computational analysis and paleogenomics of interspersed repeats in eukaryotes. In Stojanovic,N. (ed). Computational Genomics: Current Methods. Taylor & Francis, London, pp. 31-54.
-
(2007)
Computational Genomics: Current Methods
, pp. 31-54
-
-
Feschotte, C.1
Pritham, E.J.2
-
2
-
-
0024505998
-
Eukaryotic transposable elements and genome evolution
-
Finnegan,D.J. (1989) Eukaryotic transposable elements and genome evolution. Trends Genet., 5, 103-107.
-
(1989)
Trends Genet.
, vol.5
, pp. 103-107
-
-
Finnegan, D.J.1
-
3
-
-
36249023071
-
A unified classification system for eukaryotic transposable elements
-
Wicker,T., Sabot,F., Hua-Van,A. et al. (2007) A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet., 8, 973-982.
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 973-982
-
-
Wicker, T.1
Sabot, F.2
Hua-Van, A.3
-
4
-
-
0031593205
-
SINEs and LINEs share common 30 sequences: A review
-
Okada,N., Hamada,M., Ogiwara,I. et al. (1997) SINEs and LINEs share common 30 sequences: a review. Gene, 205, 229-243.
-
(1997)
Gene
, vol.205
, pp. 229-243
-
-
Okada, N.1
Hamada, M.2
Ogiwara, I.3
-
5
-
-
37549029474
-
DNA transposons and the evolution of eukaryotic genomes
-
Feschotte,C. and Pritham,E.J. (2007) DNA transposons and the evolution of eukaryotic genomes. Annu. Rev. Genet., 41, 331-368.
-
(2007)
Annu. Rev. Genet.
, vol.41
, pp. 331-368
-
-
Feschotte, C.1
Pritham, E.J.2
-
6
-
-
42349096534
-
Transposable elements and the evolution of regulatory networks
-
Feschotte,C. (2008) Transposable elements and the evolution of regulatory networks. Nat. Rev. Genet., 9, 397-405.
-
(2008)
Nat. Rev. Genet.
, vol.9
, pp. 397-405
-
-
Feschotte, C.1
-
7
-
-
36549035839
-
Discovering and detecting transposable elements in genome sequences
-
Bergman,C.M. and Quesneville,H. (2007) Discovering and detecting transposable elements in genome sequences. Brief. Bioinform., 8, 382-392.
-
(2007)
Brief. Bioinform.
, vol.8
, pp. 382-392
-
-
Bergman, C.M.1
Quesneville, H.2
-
8
-
-
34548272144
-
Genome assembly, rearrangement, and repeats
-
Tang,H. (2007) Genome assembly, rearrangement, and repeats. Chem. Rev., 38, 3391-3406.
-
(2007)
Chem. Rev.
, vol.38
, pp. 3391-3406
-
-
Tang, H.1
-
9
-
-
62549132449
-
A unified classification system for eukaryotic transposable elements should reflect their phylogeny
-
Seberg,O. and Petersen,G. (2009) A unified classification system for eukaryotic transposable elements should reflect their phylogeny. Nat. Rev. Genet., 10, 276.
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 276
-
-
Seberg, O.1
Petersen, G.2
-
10
-
-
42349111552
-
A universal classification of eukaryotic transposable elements implemented in Repbase
-
Kapitonov,V.V. and Jurka,J. (2008) A universal classification of eukaryotic transposable elements implemented in Repbase. Nat. Rev. Genet., 9, 411-412.
-
(2008)
Nat. Rev. Genet.
, vol.9
, pp. 411-412
-
-
Kapitonov, V.V.1
Jurka, J.2
-
11
-
-
77952670452
-
Identifying repeats and transposable elements in sequenced genomes: How to find your way through the dense forest of programs
-
Lerat,E. (2009) Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity (Edinb), 104, 520-533.
-
(2009)
Heredity (Edinb)
, vol.104
, pp. 520-533
-
-
Lerat, E.1
-
12
-
-
10344265019
-
A draft sequence for the genome of the domesticated silkworm (Bombyx mori)
-
Xia,Q., Zhou,Z., Lu,C. et al . (2004) A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science, 306, 1937-1940.
-
(2004)
Science
, vol.306
, pp. 1937-1940
-
-
Xia, Q.1
Zhou, Z.2
Lu, C.3
-
13
-
-
59649098867
-
Genome-wide screening and characterization of transposable elements and their distribution analysis in the silkworm, Bombyx mori
-
Osanai-Futahashi,M., Suetsugu,Y., Mita,K. et al. (2008) Genome-wide screening and characterization of transposable elements and their distribution analysis in the silkworm, Bombyx mori. Insect Biochem. Mol. Biol., 38, 1046-1057.
-
(2008)
Insect Biochem. Mol. Biol.
, vol.38
, pp. 1046-1057
-
-
Osanai-Futahashi, M.1
Suetsugu, Y.2
Mita, K.3
-
14
-
-
55449118548
-
ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun
-
Li,R., Ye,J., Li,S. et al. (2005) ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comp. Biol., 1, e43.
-
(2005)
PLoS Comp. Biol.
, vol.1
-
-
Li, R.1
Ye, J.2
Li, S.3
-
15
-
-
59649116641
-
The genome of a lepidopteran model insect, the silkworm Bombyx mori
-
Xia,Q.Y., Wang,J., Zhou,Z.Y. et al. (2008) The genome of a lepidopteran model insect, the silkworm Bombyx mori. Insect Biochem. Mol. Biol., 38, 1036-1045.
-
(2008)
Insect Biochem. Mol. Biol.
, vol.38
, pp. 1036-1045
-
-
Xia, Q.Y.1
Wang, J.2
Zhou, Z.Y.3
-
16
-
-
75549089913
-
SilkDB v2.0: A platform for silkworm (Bombyx mori) genome biology
-
Duan,J., Li,R., Cheng,D. et al. (2010) SilkDB v2.0: a platform for silkworm (Bombyx mori) genome biology. Nucleic Acids Res., 38, D453-D456.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Duan, J.1
Li, R.2
Cheng, D.3
-
17
-
-
70449713661
-
KAIKObase: An integrated silkworm genome database and data mining tool
-
Shimomura,M., Minami,H., Suetsugu,Y. et al. (2009) KAIKObase: An integrated silkworm genome database and data mining tool. BMC Genomics, 10, 486.
-
(2009)
BMC Genomics
, vol.10
, pp. 486
-
-
Shimomura, M.1
Minami, H.2
Suetsugu, Y.3
-
18
-
-
23844525077
-
Repbase Update, a database of eukaryotic repetitive elements
-
Jurka,J., Kapitonov,V.V., Pavlicek,A. et al. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res., 110, 462-467.
-
(2005)
Cytogenet. Genome Res.
, vol.110
, pp. 462-467
-
-
Jurka, J.1
Kapitonov, V.V.2
Pavlicek, A.3
-
19
-
-
77957118462
-
Burst expansion, distribution and diversification of MITEs in the silkworm genome
-
Han,M.J., Shen,Y.-H., Gao,Y.-H. et al. (2010) Burst expansion, distribution and diversification of MITEs in the silkworm genome. BMC Genomics, 11, 520.
-
(2010)
BMC Genomics
, vol.11
, pp. 520
-
-
Han, M.J.1
Shen, Y.-H.2
Gao, Y.-H.3
-
20
-
-
77649334384
-
BmSE, a SINE family with 3′ ends of (ATTT) repeats in domesticated silkworm (Bombyx mori)
-
Xu,J., Liu,T., Li,D. et al. (2010) BmSE, a SINE family with 3′ ends of (ATTT) repeats in domesticated silkworm (Bombyx mori). J Genet Genomics, 37, 125-135.
-
(2010)
J Genet Genomics
, vol.37
, pp. 125-135
-
-
Xu, J.1
Liu, T.2
Li, D.3
-
22
-
-
0037433054
-
LTR-STRUC: A novel search and identification program for LTR retrotransposons
-
McCarthy,E.M. and McDonald,J.F. (2003) LTR-STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics, 19, 362-367.
-
(2003)
Bioinformatics
, vol.19
, pp. 362-367
-
-
McCarthy, E.M.1
McDonald, J.F.2
-
23
-
-
34547592867
-
LTR-FINDER: An efficient tool for the prediction of full-length LTR retrotransposons
-
Xu,Z. and Wang,H. (2007) LTR-FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res., 35, W265-W268.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Xu, Z.1
Wang, H.2
-
24
-
-
75649096724
-
MGEScan-non-LTR: Computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes
-
Rho,M. and Tang,H. (2009) MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes. Nucleic Acids Res., 37, e143.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Rho, M.1
Tang, H.2
-
25
-
-
23844519396
-
Survey of long terminal repeat retrotransposons of domesticated silkworm (Bombyx mori)
-
Xu,J.S., Xia,Q.Y., Li,J. et al. (2005) Survey of long terminal repeat retrotransposons of domesticated silkworm (Bombyx mori). Insect Biochem. Mol. Biol., 35, 921-929.
-
(2005)
Insect Biochem. Mol. Biol.
, vol.35
, pp. 921-929
-
-
Xu, J.S.1
Xia, Q.Y.2
Li, J.3
-
26
-
-
70450250730
-
FastPCR software for PCR primer and probe design and repeat search
-
Kalendar,R., Lee,D. and Schulman,A.H. (2009) FastPCR software for PCR primer and probe design and repeat search. Genes Genomes Genomics, 3, 1-14.
-
(2009)
Genes Genomes Genomics
, vol.3
, pp. 1-14
-
-
Kalendar, R.1
Lee, D.2
Schulman, A.H.3
-
27
-
-
33846224659
-
Improved repeat identification and masking in Dipterans
-
Smith,C.D., Edgar,R.C., Yandell,M.D. et al. (2007) Improved repeat identification and masking in Dipterans. Gene, 389, 1-9.
-
(2007)
Gene
, vol.389
, pp. 1-9
-
-
Smith, C.D.1
Edgar, R.C.2
Yandell, M.D.3
-
28
-
-
84860513986
-
PILER: Identification and classification of genomic repeats
-
Edgar,R.C. and Myers,E.W. (2005) PILER: identification and classification of genomic repeats. Bioinformatics, 21 (Suppl 1), i152-i158.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Edgar, R.C.1
Myers, E.W.2
-
29
-
-
0033555906
-
Tandem repeats finder: A program to analyze DNA sequences
-
Benson,G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res., 27, 573-580.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 573-580
-
-
Benson, G.1
-
30
-
-
33750831582
-
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor
-
Kohany,O., Gentles,A.J., Hankus,L. et al. (2006) Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics, 7, 474.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 474
-
-
Kohany, O.1
Gentles, A.J.2
Hankus, L.3
-
31
-
-
65549101705
-
TEclass - A tool for automated classification of unknown eukaryotic transposable elements
-
Abrusan,G., Grundmann,N., DeMester,L. et al. (2009) TEclass-a tool for automated classification of unknown eukaryotic transposable elements. Bioinformatics, 25, 1329-1330.
-
(2009)
Bioinformatics
, vol.25
, pp. 1329-1330
-
-
Abrusan, G.1
Grundmann, N.2
DeMester, L.3
-
32
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul,S.F., Madden,T.L., Schaffer,A.A. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
-
33
-
-
0034201441
-
EMBOSS: The European Molecular Biology Open Software Suite
-
Rice,P., Longden,I. and Bleasby,A. (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet., 16, 276-277.
-
(2000)
Trends Genet.
, vol.16
, pp. 276-277
-
-
Rice, P.1
Longden, I.2
Bleasby, A.3
-
34
-
-
79959931985
-
HMMER web server: Interactive sequence similarity searching
-
Finn,R.D., Clements,J. and Eddy,S.R. (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res., 39, W29-W37.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Finn, R.D.1
Clements, J.2
Eddy, S.R.3
-
35
-
-
34247877564
-
De novo identification of LTR retrotransposons in eukaryotic genomes
-
Rho,M., Choi,J.H., Kim,S. et al. (2007) De novo identification of LTR retrotransposons in eukaryotic genomes. BMC Genomics, 8, 90.
-
(2007)
BMC Genomics
, vol.8
, pp. 90
-
-
Rho, M.1
Choi, J.H.2
Kim, S.3
|