The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences
Open accessAbstract
Miniature inverted-repeat transposable elements (MITEs) are a special type of Class 2 non-autonomous transposable element (TE) that are abundant in the non-coding regions of the genes of many plant and animal species. The accurate identification of MITEs has been a challenge for existing programs because they lack coding sequences and, as such, evolve very rapidly. Because of their importance to gene and genome evolution, we developed MITE-Hunter, a program pipeline that can identify MITEs as well as other small Class 2 non-autonomous TEs from genomic DNA data sets. The output of MITE-Hunter is composed of consensus TE sequences grouped into families that can be used as a library file for homology-based TE detection programs such as RepeatMasker. MITE-Hunter was evaluated by searching the rice genomic database and comparing the output with known rice TEs. It discovered most of the previously reported rice MITEs (97.6%), and found sixteen new elements. MITE-Hunter was also compared with two other MITE discovery programs, FINDMITE and MUST. Unlike MITE-Hunter, neither of these programs can search large genomic data sets including whole genome sequences. More importantly, MITE-Hunter is significantly more accurate than either FINDMITE or MUST as the vast majority of their outputs are false-positives.
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Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
Cited by
RepeatModeler2 for automated genomic discovery of transposable element families
Flynn, J. M., Hubley, R., Goubert, C., Rosen, J., Clark, A. G., Feschotte, C., & Smit, A. F. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1921046117 · Cited by 3,848
Improved maize reference genome with single-molecule technologies
Jiao, Y., Peluso, P., Shi, J., Liang, T., Stitzer, M. C., Wang, B., Campbell, M. S., Stein, J. C., Wei, X., Chin, C.-S., et al. (2017) · Nature · doi:10.1038/nature22971 · Cited by 1,210
A beginner’s guide to eukaryotic genome annotation
Yandell, M., & Ence, D. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3174 · Cited by 588
Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations
Qin, P., Lu, H., Du, H., Wang, H., Chen, W., Chen, Z., He, Q., Ou, S., Zhang, H., Li, X., et al. (2021) · Cell · doi:10.1016/j.cell.2021.04.046 · Cited by 578
Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis
Griesmann, M., Chang, Y., Liu, X., Song, Y., Haberer, G., Crook, M. B., Billault-Penneteau, B., Lauressergues, D., Keller, J., Imanishi, L., et al. (2018) · Science · doi:10.1126/science.aat1743 · Cited by 429
Metadata
- Authors
- Han, Y., & Wessler, S. R.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-09-29
- Volume
- 38
- Issue
- 22
- Pages
- e199-e199
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2134783286
- Cited by
- 631
- References
- 2
- FWCI
- 11.28
- Type
- journal article
- Language
- en
- Open access
- gold
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