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

2. LTR Retroelement LTR SHORT INVERTED REPEATS FLANK LTRHOST REPEATS

3. LTR Retroelement

4. TIRs GAGTAAAATGCAAGAAACCCACTTTGAAGGCTAGGTTTGCAGATAACACTA CGTTACATTTTTTGGACAGAAAGCACCACGTCTCGTGTAATCTTGTTGCAA ATAACACTGATTGGCGGATTAGAGCGCTTAAAGTATGTTTATGACAGGAGG GTCCAGATTTTGCCCTTGTGGCGTAACGGCTTGGCCATGACGGCGT ------> <------ ACGCCGTTTCGCCCCAAGCCGTTATGTCACATGGGCAAAATCTGGAACCAC CTGTCATAAACACACTTAAAGCACTCTAATCCGCCAATCAGTGTTATTTGC AATAAGATTACACAAAACGTGATGCTTTTTGTTCAAAAAATGTAACGTAGT GTTATCTGCAAACCTAGCCTTCAAAATGGTGGTTTTATGCAATTTACTC Reverse complement

5. SOLO LTRs LTR SHORT INVERTED REPEATS FLANK LTRHOST REPEATS

6. Example Retroelement Annotation

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

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