The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Discovering and detecting transposable elements in genome sequences
Open accessAbstract
The contribution of transposable elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis. Here we review the diversity of innovative approaches to identify and annotate TEs in the post-genomic era, covering both the discovery of new TE families and the detection of individual TE copies in genome sequences. These approaches span a broad spectrum in computational biology including de novo, homology-based, structure-based and comparative genomic methods. We conclude that the integration and visualization of multiple approaches and the development of new conceptual representations for TE annotation will further advance the computational analysis of this dynamic component of the genome.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Tandem repeats finder: a program to analyze DNA sequences
Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
Versatile and open software for comparing large genomes
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254
Mobile Elements: Drivers of Genome Evolution
Kazazian, H. H. (2004) · Science · doi:10.1126/science.1089670 · Cited by 1,922
Fast algorithms for large-scale genome alignment and comparison
Delcher, A. L. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.11.2478 · Cited by 1,036
Synergy between sequence and size in Large-scale genomics
Gregory, T. R. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1674 · Cited by 348
Molecular archeology of L1 insertions in the human genome
Szak, S. T., Pickeral, O. K., Makalowski, W., Boguski, M. S., Landsman, D., & Boeke, J. D. (2002) · Genome Biology · doi:10.1186/gb-2002-3-10-research0052 · Cited by 230 · cited 1×
“For example, TSDs can be used to refine the precise location of TEs, as is implemeted in TSDfinder [75] or SINEDR [76].”
Method
Cited by
A beginner’s guide to eukaryotic genome annotation
Yandell, M., & Ence, D. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3174 · Cited by 588
Tørresen, O. K., Star, B., Mier, P., Andrade-Navarro, M. A., Bateman, A., Jarnot, P., Gruca, A., Grynberg, M., Kajava, A. V., Promponas, V. J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz841 · Cited by 347
PASTEC: An Automatic Transposable Element Classification Tool
Hoede, C., Arnoux, S., Moisset, M., Chaumier, T., Inizan, O., Jamilloux, V., & Quesneville, H. (2014) · PLoS ONE · doi:10.1371/journal.pone.0091929 · Cited by 310
Self-citationTransposable element detection from whole genome sequence data
Ewing, A. D. (2015) · Mobile DNA · doi:10.1186/s13100-015-0055-3 · Cited by 155
A call for benchmarking transposable element annotation methods
Hoen, D. R., Hickey, G., Bourque, G., Casacuberta, J., Cordaux, R., Feschotte, C., Fiston-Lavier, A.-S., Hua-Van, A., Hubley, R., Kapusta, A., et al. (2015) · Mobile DNA · doi:10.1186/s13100-015-0044-6 · Cited by 105
Self-citation
Metadata
- Authors
- Bergman, C. M., & Quesneville, H.
- Venue
- Briefings in Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-05-04
- Volume
- 8
- Issue
- 6
- Pages
- 382-392
- ISSN
- 1467-5463 (ISSN-L)
- 1477-4054
- OpenAlex
- W2129581281
- Cited by
- 258
- References
- 7
- FWCI
- 9.63
- Type
- journal article
- Language
- en
- Open access
- bronze
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Discovering and detecting transposable elements in genome sequences. https://app.cochat.ai/papers/10.1093/bib/bbm048
- The paper
- Bergman, C. M., & Quesneville, H. (2007). Discovering and detecting transposable elements in genome sequences. Briefings in Bioinformatics. https://doi.org/10.1093/bib/bbm048
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
