文章“MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences.”
文章地址：https://academic.oup.com/nar/article/38/22/e199/1048972
文章内容：
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.
MITE 存在于基因的非编码区。
In plants, six Class 2 superfamilies have been identified thus far: Tc1/Mariner, PIF/Harbinger, hAT, MULE, CACTA and Helitron (5,6). With the exception of Helitrons, TEs in the other five superfamilies have terminal inverted repeats (TIRs) and transpose through a cut-and-paste mechanism.
DNA转座子在植物中有6个超家族。
Miniature inverted-repeat TEs (MITEs) are a special type of Class 2 non-autonomous element that is present in high copy numbers in many eukaryotic genomes.
MITEs是与上面提到的6个超家族重叠的，就是说有的DNA转座子是MITE同时也属于6个超家族的某个超家族。
Many TE annotation programs have been developed that use one or more of the following computational approaches: (i) homology-based, (ii) de novo, (iii) polymorphism based and (iv) structure based (21–23).
TE鉴定的四种方法。
MITE-Hunter pipeline：
(i) identify TE candidates through a structure-based approach, (ii) identify and filter false-positives using an approach based on the pairwise sequence alignment (PSA), (iii) generate exemplars, (iv) identify and filter false-positives using an approach based on the multiple sequence alignment (MSA), generate consensus sequences and predict TSDs and (v) group consensus sequences into families.
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