Repeat Elements Repeat Modeler Repeat Masker LTRFINDER 2020

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Repeat Elements Repeat. Modeler & Repeat. Masker LTR_FINDER 2020 workshop Presenter: Yingyi Yang

Repeat Elements Repeat. Modeler & Repeat. Masker LTR_FINDER 2020 workshop Presenter: Yingyi Yang

Content Repeat Element Repeatmodeler Repeatmasker LTR-FINDER

Content Repeat Element Repeatmodeler Repeatmasker LTR-FINDER

01 Repeat Elements What? Types? Diferences? Why

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

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

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

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

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

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

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

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

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

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

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

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:

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

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

2020 Thanks Repeat Elements

2020 Thanks Repeat Elements