Lab 5 – Comparative Genomics
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).
Hwk 4 - Problem 4 Retroelement Annotation
LTR Retroelement
SOLO LTRs
• For more information check section on Mobile Genetic Elements in Genomes3 by Brown: http://books.google.com/books?id=Cjl98tqp6rsC&lpg=PP1&pg=PA256#v=onepage&q=Mobile%20Genetic%20Elements&f=false
TIRs
GAGTAAAATGCAAGAAACCCACTTTGAAGGCTAGGTTTGCAGATAACACTACGTTACATTTTTTGGACAGAAAGCACCACGTCTCGTGTAATCTTGTTGCAAATAACACTGATTGGCGGATTAGAGCGCTTAAAGTATGTTTATGACAGGAGGGTCCAGATTTTGCCCTTGTGGCGTAACGGCTTGGCCATGACGGCGT------>
<------ACGCCGTTTCGCCCCAAGCCGTTATGTCACATGGGCAAAATCTGGAACCACCTGTCATAAACACACTTAAAGCACTCTAATCCGCCAATCAGTGTTATTTGCAATAAGATTACACAAAACGTGATGCTTTTTGTTCAAAAAATGTAACGTAGTGTTATCTGCAAACCTAGCCTTCAAAATGGTGGTTTTATGCAATTTACTC
Reverse complement
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
Hwk5 – Problem 5 – Complete Annotation
FINAL RESULT