Repeat Elements Repeat Modeler Repeat Masker LTRFINDER 2020
- Slides: 19
Repeat Elements Repeat. Modeler & Repeat. Masker LTR_FINDER 2020 workshop Presenter: Yingyi Yang
Content Repeat Element Repeatmodeler Repeatmasker LTR-FINDER
01 Repeat Elements What? Types? Diferences? Why
Repeat Elements tandem repeats 串联重复 Satellite DNA 卫星DNA Minisatellite Microsatellite interspersed repeats散布重复 class-II:Transposons转座子 Transposable elements(TEs) class-I:Retrotransposons反转座子 转座元件
Repeat Elements Minisatellite小卫星—— 10 -60 bp 单一型(pure) Microsatellite 微卫星 —— 2 -10 bp ATATATATAT 复合型(compound) ATATATCACACAC 间断型(interrupted) ATATATCAA Simple Sequence Repeat(SSR)简单重复序列 Short tandem repeat(STR)简单串联序列
PCR primer/Breeding/paternity testing/individual identification restriction enzyme gel electrophoresis
Transposable elements Transposons encode the protein transposase RNA ——cut a nd paste transposase Retrotransposon L T R r e t r o t r a n sc. DNA posons Non-LTR retrotransposons function via reverse transcription ——copy and paste similar to retroviruses, such as HIV
Retrotransposon LTR —— Long terminal repeats LTR retrotransposons LINE ——Long INterspersed Elements Non-LTR SINE ——Short INterspersed Elements
Comparison widespread structure function LINE eukaryotes longer 2 * ORF 2 * UTR autonomous retroelements, enlarge the genome SINE eukaryotes shorter non-autonomous retrotransposons. untranslated region (UTR) that includes an RNA polymerase II promoter 5' UTR contains the promoter sequence, 3' UTR contains a polyadenylation signal (AATAAA) and a poly-A tail ORF——open reading frame lack LTR, most are inactive, "junk DNA" ORF - open reading frame RNA binding protein endonuclease/reverse transcriptase
is the mainly responsible for genome enlargement TIR: terminal inverted repeat. 反向重复序列 Because of accumulated mutations, most retrotransposons are no longer able to retrotranspose
Repeat Elements Satellite DNA Minisatellite Microsatellite(SSR、STR) Transposable elements(TEs) Transposons pure compound interrupted HERV LTR Retrotransposon MER 4 retroposon LINE Non-LTR SINE LINE 1 LINE 2 Alu MIR
Why we analysis Repeat Elements ? Transposable elements u abundant u induce mutations— functionalization u related to desease Satellite DNA u reduce repeat frequency u Appendages regeneration u Human genome: 42% —— retrotransposons 2– 3% —— transposons 镰刀型贫血 sickle cell anemia
02 Software
Software u. Algorithm: u. Repeat. Modeler可用来从头对基因组的 unhmmer、cross_match、 u. Repeat. Modeler u. Reapeat. Masker 重复序列家族进行建模注释,它的核 ABBlast/WUBlast、 心组件是RECON和Repat. Scout。 RMBlast 、Decypher u. Library-based: 通过相似性比对来识别重复序列,可以 屏蔽序列中转座子重复序列和低复杂度 序列(默认将其替换成N)
Usage 1 Install 2 Input fasta System: Cent OS https: //www. centos. org install: conda yum install conda https: //docs. conda. io/en/latest/miniconda. html install: Repeat. Masker, Repeat. Modeler http: //www. repeatmasker. org/Repeat. Modeler/ Output 4 http: //repeatmasker. org/ 5 Input fasta n → 1 file 6 3 Process Repeat. Modeler Process Repeat. Masker Result
Software u. Select possible LTR pairs utrace through it upstream and u. LTR_FINDER downstreams as long as there‘re high similarity ufind signals in near LTR region ugather informations
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