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).

LTR Retroelement

LTR

SHORT INVERTED REPEATS FLANK LTRHOST REPEATS

LTR Retroelement

TIRs

GAGTAAAATGCAAGAAACCCACTTTGAAGGCTAGGTTTGCAGATAACACTACGTTACATTTTTTGGACAGAAAGCACCACGTCTCGTGTAATCTTGTTGCAAATAACACTGATTGGCGGATTAGAGCGCTTAAAGTATGTTTATGACAGGAGGGTCCAGATTTTGCCCTTGTGGCGTAACGGCTTGGCCATGACGGCGT------>

<------ACGCCGTTTCGCCCCAAGCCGTTATGTCACATGGGCAAAATCTGGAACCACCTGTCATAAACACACTTAAAGCACTCTAATCCGCCAATCAGTGTTATTTGCAATAAGATTACACAAAACGTGATGCTTTTTGTTCAAAAAATGTAACGTAGTGTTATCTGCAAACCTAGCCTTCAAAATGGTGGTTTTATGCAATTTACTC

Reverse complement

SOLO LTRs

LTR

SHORT INVERTED REPEATS FLANK LTRHOST REPEATS

Example Retroelement Annotation

FINAL RESULT

Gypsy, WHAM

TIR, Mutator, Annie

SOLO LTR, Copia, WIS

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

Complete Annotation – Identify Retros

Complete Annotation – Identify Genes

FINAL RESULT