annotating retroelements

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Annotating Retroelements. Dotter , identify direct and inverted repeats, and graphically visualize them. (R ough idea of coordinates – highlight in your sequence, and write it down to keep as your “map”) - PowerPoint PPT Presentation

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  • Annotating RetroelementsDotter, identify direct and inverted repeats, and graphically visualize them. (Rough idea of coordinates highlight in your sequence, and write it down to keep as your map)

    TREP, identify the repetitive elements and their location in the sequence. (BLAST WHOLE Sequence. Remember to select the complete set and unselect the filter.)

    Blast2sequences between the two halves of the sequence, to more precisely identify the borders of the repeats (LTRs).

  • LTR Retroelement

  • LTR Retroelement

  • TIRsGAGTAAAATGCAAGAAACCCACTTTGAAGGCTAGGTTTGCAGATAACACTACGTTACATTTTTTGGACAGAAAGCACCACGTCTCGTGTAATCTTGTTGCAAATAACACTGATTGGCGGATTAGAGCGCTTAAAGTATGTTTATGACAGGAGGGTCCAGATTTTGCCCTTGTGGCGTAACGGCTTGGCCATGACGGCGT------>

  • SOLO LTRs

  • Example Retroelement Annotation

  • FINAL RESULTGypsy, WHAM TIR, Mutator, Annie SOLO LTR, Copia, WIS

  • Annotating Complete SequencesDotterTREP, Blast2sequences

    BLASTX sequence that does not include repetitive elements. Identify possible proteins in your sequence.BLASTn est_others, support predicted proteins with real ESTsFGENESH+ polish your gene borders and structureBLASTp validate your predicted protein with related one from BLASTx

  • Complete Annotation Identify Retros

  • Complete Annotation Identify Genes

  • FINAL RESULT

    MITE : miniature inverted repeat transposable elements*