lab 5 – comparative genomics

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