基因组的注释20131127.pdfx.pdf

Genome annotation Analysis Min Xie xiemin@ Genome annotation 1 Repeat annotation 2 Gene annotation 33 Pseudogene annotation 44 Function annotation 5 3 Non-coding RNA annotation Genome annotation 1 Repeat annotation 2 Gene annotation 33 Pseudogene annotation 44 Function annotation 5 3 Non-coding RNA annotation Repeat annotation • Tandem repeats (satellite) Copy 2 Copy 1 Copy 3 • Dispersed repeats (transposons) Copy 1 Copy 2 Copy 3 Tandem repeats Classify based on unit size: – Satellite (unit 100bp) – Minisatellite (10bp unit = 100bp) – Microsatellite (unit = 10bp) Available softwares: – TRF: de novo prediction /trf/trf.html – Repeatmasker -noint: library based / Dispersed repeats Transposon also named: TE (Transposable element) Classification based on mRNA intermediate • Class I: retrotransopons, copy and paste include LTR, LINE, SINE, PLE, DIR • Class II: DNA transposons • Subclass I: cut and paste include TIR and Crypton • Subclass II: copy and paste, rolling cycle, include Helitron and Maverick. Reference: Thomas Wicker, et.al. A unified classification system for eukaryotic transposable elements. 2007. Nature Reviews Genetics. volume 8 | 973 Methods and softwares De novo prediction: LTR_Finder (predict LTR retrotransposons by structure characters) Alignment by DNA conservation: RepeatMasker (against Repbase TE or species-specific library) Alignment by protein conservation: RepeatProteinMask (against TE