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Annotating Retroelements

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”)

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Annotating Retroelements

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  1. Annotating Retroelements • Dotter, 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.) • Blast2sequencesbetween the two halves of the sequence, to more precisely identify the borders of the repeats (LTRs).

  2. LTR Retroelement LTR HOST REPEATS SHORT INVERTED REPEATS FLANK LTR

  3. LTR Retroelement

  4. TIRs Reverse complement GAGTAAAATGCAAGAAACCCACTTTGAAGGCTAGGTTTGCAGATAACACTACGTTACATTTTTTGGACAGAAAGCACCACGTCTCGTGTAATCTTGTTGCAAATAACACTGATTGGCGGATTAGAGCGCTTAAAGTATGTTTATGACAGGAGGGTCCAGATTTTGCCCTTGTGGCGTAACGGCTTGGCCATGACGGCGT ------> <------ ACGCCGTTTCGCCCCAAGCCGTTATGTCACATGGGCAAAATCTGGAACCACCTGTCATAAACACACTTAAAGCACTCTAATCCGCCAATCAGTGTTATTTGCAATAAGATTACACAAAACGTGATGCTTTTTGTTCAAAAAATGTAACGTAGTGTTATCTGCAAACCTAGCCTTCAAAATGGTGGTTTTATGCAATTTACTC

  5. SOLO LTRs LTR HOST REPEATS SHORT INVERTED REPEATS FLANK LTR

  6. Example Retroelement Annotation

  7. FINAL RESULT Gypsy, WHAM SOLO LTR, Copia, WIS TIR, Mutator, Annie

  8. Annotating Complete Sequences • Dotter • TREP, Blast2sequences • BLASTX – sequence that does not include repetitive elements. Identify possible proteins in your sequence. • BLASTn – est_others, support predicted proteins with real ESTs • FGENESH+ – polish your gene borders and structure • BLASTp– validate your predicted protein with related one from BLASTx

  9. Complete Annotation – Identify Retros

  10. Complete Annotation – Identify Genes

  11. FINAL RESULT

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