Transcript Homework Averages - University of California, Davis

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
HOST REPEATS
SHORT INVERTED REPEATS FLANK LTR
LTR Retroelement
TIRs
Reverse complement
GAGTAAAATGCAAGAAACCCACTTTGAAGGCTAGGTTTGCAGATAACACTA
CGTTACATTTTTTGGACAGAAAGCACCACGTCTCGTGTAATCTTGTTGCAA
ATAACACTGATTGGCGGATTAGAGCGCTTAAAGTATGTTTATGACAGGAGG
GTCCAGATTTTGCCCTTGTGGCGTAACGGCTTGGCCATGACGGCGT
------>
<-----ACGCCGTTTCGCCCCAAGCCGTTATGTCACATGGGCAAAATCTGGAACCAC
CTGTCATAAACACACTTAAAGCACTCTAATCCGCCAATCAGTGTTATTTGC
AATAAGATTACACAAAACGTGATGCTTTTTGTTCAAAAAATGTAACGTAGT
GTTATCTGCAAACCTAGCCTTCAAAATGGTGGTTTTATGCAATTTACTC
SOLO LTRs
LTR
HOST REPEATS
SHORT INVERTED REPEATS FLANK LTR
Example Retroelement Annotation
FINAL RESULT
Gypsy, WHAM
SOLO LTR, Copia, WIS
TIR, Mutator, Annie
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