173 related articles for article (PubMed ID: 38373163)
1. The good, the bad and the ugly of transposable elements annotation tools.
Loreto ELS; Melo ES; Wallau GL; Gomes TMFF
Genet Mol Biol; 2024; 46(3 Suppl 1):e20230138. PubMed ID: 38373163
[TBL] [Abstract][Full Text] [Related]
2. Transposable element annotation of the rice genome.
Juretic N; Bureau TE; Bruskiewich RM
Bioinformatics; 2004 Jan; 20(2):155-60. PubMed ID: 14734305
[TBL] [Abstract][Full Text] [Related]
3. Preparation of Non-overlapping Transposable Elements (TEs) Annotation by Interval Tree.
Kojima S
Methods Mol Biol; 2022; 2509():353-360. PubMed ID: 35796974
[TBL] [Abstract][Full Text] [Related]
4. A new approach for annotation of transposable elements using small RNA mapping.
El Baidouri M; Kim KD; Abernathy B; Arikit S; Maumus F; Panaud O; Meyers BC; Jackson SA
Nucleic Acids Res; 2015 Jul; 43(13):e84. PubMed ID: 25813049
[TBL] [Abstract][Full Text] [Related]
5. RepBox: a toolbox for the identification of repetitive elements.
Burkes-Patton S; Cooper EA; Schlueter J
BMC Bioinformatics; 2023 Aug; 24(1):317. PubMed ID: 37608271
[TBL] [Abstract][Full Text] [Related]
6. TEnest: automated chronological annotation and visualization of nested plant transposable elements.
Kronmiller BA; Wise RP
Plant Physiol; 2008 Jan; 146(1):45-59. PubMed ID: 18032588
[TBL] [Abstract][Full Text] [Related]
7. Combined evidence annotation of transposable elements in genome sequences.
Quesneville H; Bergman CM; Andrieu O; Autard D; Nouaud D; Ashburner M; Anxolabehere D
PLoS Comput Biol; 2005 Jul; 1(2):166-75. PubMed ID: 16110336
[TBL] [Abstract][Full Text] [Related]
8. Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes.
Janicki M; Rooke R; Yang G
Chromosome Res; 2011 Aug; 19(6):787-808. PubMed ID: 21850457
[TBL] [Abstract][Full Text] [Related]
9. Exploring repetitive DNA landscapes using REPCLASS, a tool that automates the classification of transposable elements in eukaryotic genomes.
Feschotte C; Keswani U; Ranganathan N; Guibotsy ML; Levine D
Genome Biol Evol; 2009 Jul; 1():205-20. PubMed ID: 20333191
[TBL] [Abstract][Full Text] [Related]
10. An Overview of Best Practices for Transposable Element Identification, Classification, and Annotation in Eukaryotic Genomes.
Rodriguez F; Arkhipova IR
Methods Mol Biol; 2023; 2607():1-23. PubMed ID: 36449155
[TBL] [Abstract][Full Text] [Related]
11. A Tutorial of EDTA: Extensive De Novo TE Annotator.
Su W; Ou S; Hufford MB; Peterson T
Methods Mol Biol; 2021; 2250():55-67. PubMed ID: 33900591
[TBL] [Abstract][Full Text] [Related]
12. Characterization and functional annotation of nested transposable elements in eukaryotic genomes.
Gao C; Xiao M; Ren X; Hayward A; Yin J; Wu L; Fu D; Li J
Genomics; 2012 Oct; 100(4):222-30. PubMed ID: 22800764
[TBL] [Abstract][Full Text] [Related]
13. TE-Tracker: systematic identification of transposition events through whole-genome resequencing.
Gilly A; Etcheverry M; Madoui MA; Guy J; Quadrana L; Alberti A; Martin A; Heitkam T; Engelen S; Labadie K; Le Pen J; Wincker P; Colot V; Aury JM
BMC Bioinformatics; 2014 Nov; 15(1):377. PubMed ID: 25408240
[TBL] [Abstract][Full Text] [Related]
14. TIR-Learner, a New Ensemble Method for TIR Transposable Element Annotation, Provides Evidence for Abundant New Transposable Elements in the Maize Genome.
Su W; Gu X; Peterson T
Mol Plant; 2019 Mar; 12(3):447-460. PubMed ID: 30802553
[TBL] [Abstract][Full Text] [Related]
15. Roadmap for annotating transposable elements in eukaryote genomes.
Permal E; Flutre T; Quesneville H
Methods Mol Biol; 2012; 859():53-68. PubMed ID: 22367865
[TBL] [Abstract][Full Text] [Related]
16. A call for benchmarking transposable element annotation methods.
Hoen DR; Hickey G; Bourque G; Casacuberta J; Cordaux R; Feschotte C; Fiston-Lavier AS; Hua-Van A; Hubley R; Kapusta A; Lerat E; Maumus F; Pollock DD; Quesneville H; Smit A; Wheeler TJ; Bureau TE; Blanchette M
Mob DNA; 2015; 6():13. PubMed ID: 26244060
[TBL] [Abstract][Full Text] [Related]
17. Genomic re-assessment of the transposable element landscape of the potato genome.
Zavallo D; Crescente JM; Gantuz M; Leone M; Vanzetti LS; Masuelli RW; Asurmendi S
Plant Cell Rep; 2020 Sep; 39(9):1161-1174. PubMed ID: 32435866
[TBL] [Abstract][Full Text] [Related]
18. Modeling transposable element dynamics with fragmentation equations.
Banuelos M; Sindi S
Math Biosci; 2018 Aug; 302():46-66. PubMed ID: 29787745
[TBL] [Abstract][Full Text] [Related]
19. Efficient homology-based annotation of transposable elements using minimizers.
Gonzalez-García LN; Lozano-Arce D; Londoño JP; Guyot R; Duitama J
Appl Plant Sci; 2023; 11(4):e11520. PubMed ID: 37601317
[TBL] [Abstract][Full Text] [Related]
20. Transposome: a toolkit for annotation of transposable element families from unassembled sequence reads.
Staton SE; Burke JM
Bioinformatics; 2015 Jun; 31(11):1827-9. PubMed ID: 25644271
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]