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MITE-Hunter specifications


Unique identifier OMICS_03533
Name MITE-Hunter
Alternative name mitehunter
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for MITE-Hunter

MITE-Hunter in publications

PMCID: 5950925
PMID: 29659815
DOI: 10.1093/gbe/evy073

[…] were searched against both strands of the peach genome. microsatellites (word composed exclusively of 1-, 2-, or 3 nt-period repeats) were removed from analysis., mite prediction was performed with mite-hunter (). about 262 and 241 consensus sequences, with its multiple sequence alignments (msa) associated, were obtained for peach and p. mume, respectively. as mite-hunter manual recommends, […]

PMCID: 5750206
PMID: 29296019
DOI: 10.1038/s41467-017-02546-5

[…] haplotype-specific indels were verified through alignment of raw pacbio reads spanning the boundary regions in both haplotypes., non-autonomous dna transposons in s. lepidophylla were identified by mite-hunter and were classified according to the sequence of termini and length of target site duplication (tsd) provided in the output from mite-hunter based on the guide of zhao et al.. candidate […]

PMCID: 5801600
PMID: 29253147
DOI: 10.1093/gigascience/gix124

[…] including long terminal repeat retrotransposons (ltr-rts; e.g., gypsy and copia) (fig. ), non-ltr retrotransposons, and dna transposons, using repeatmodeler (repeatmodeler, rrid:scr_015027) [], mite_hunter [], and ltr_retriever []. most repetitive elements are unassembled, incomplete, or collapsed in short-read-based reference genomes, which results in the underestimation of the repeat […]

PMCID: 5737489
PMID: 28922823
DOI: 10.1093/gigascience/gix065

[…] the gene models using additional genome-guided transcript assembly evidence to generate a high-quality gene model set. we first created a c. acuminata specific custom repeat library (crl) using mite-hunter v. 2011 [] and repeatmodeler v. 1.0.8 (repeatmodeler, rrid:scr_015027) []. protein coding genes were removed from each repeat library using v. 1.1 [] and combined […]

PMCID: 5458060
PMID: 28537264
DOI: 10.1038/ncomms15275

[…] by screening the assembled spinach genome using ltrharvest (v1.5.7; parameters ‘-minlenltr 100 -maxlenltr 6000 -mindistltr 1500 -maxdistltr 25000 -mintsd 5 -maxtsd 5 -motif tgca -vic 10') and mite-hunter (v11-2011; parameters ‘-n 20 -c 50'), respectively. the spinach genome was then masked using repeatmasker (v4.0.5; with the ltr retrotransposon and mite […]

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MITE-Hunter institution(s)
Department of Plant Biology, University of Georgia, Athens, GA, USA

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