annotating retroelements
DESCRIPTION
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 PresentationTRANSCRIPT
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