MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences
Open Access
- 29 September 2010
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 38 (22), e199
- https://doi.org/10.1093/nar/gkq862
Abstract
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.Keywords
This publication has 33 references indexed in Scilit:
- Tuned for Transposition: Molecular Determinants Underlying the Hyperactivity of a Stowaway MITEScience, 2009
- TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequencesNucleic Acids Research, 2009
- The Sorghum bicolor genome and the diversification of grassesNature, 2009
- Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEsGenome Research, 2008
- The Rice Annotation Project Database (RAP-DB): 2008 updateNucleic Acids Research, 2007
- Dramatic amplification of a rice transposable element during recent domesticationProceedings of the National Academy of Sciences of the United States of America, 2006
- MUSCLE: multiple sequence alignment with high accuracy and high throughputNucleic Acids Research, 2004
- Initial sequencing and comparative analysis of the mouse genomeNature, 2002
- Initial sequencing and analysis of the human genomeNature, 2001
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997