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Lab 5 – Comparative Genomics

Lab 5 – Comparative Genomics. 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”)

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Lab 5 – Comparative Genomics

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  1. Lab 5 – Comparative Genomics

  2. 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.) • Blast2sequencesbetween the two halves of the sequence, to more precisely identify the borders of the repeats (LTRs).

  3. Hwk 4 - Problem 4 Retroelement Annotation

  4. LTR Retroelement

  5. 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

  6. TIRs Reverse complement GAGTAAAATGCAAGAAACCCACTTTGAAGGCTAGGTTTGCAGATAACACTACGTTACATTTTTTGGACAGAAAGCACCACGTCTCGTGTAATCTTGTTGCAAATAACACTGATTGGCGGATTAGAGCGCTTAAAGTATGTTTATGACAGGAGGGTCCAGATTTTGCCCTTGTGGCGTAACGGCTTGGCCATGACGGCGT ------> <------ ACGCCGTTTCGCCCCAAGCCGTTATGTCACATGGGCAAAATCTGGAACCACCTGTCATAAACACACTTAAAGCACTCTAATCCGCCAATCAGTGTTATTTGCAATAAGATTACACAAAACGTGATGCTTTTTGTTCAAAAAATGTAACGTAGTGTTATCTGCAAACCTAGCCTTCAAAATGGTGGTTTTATGCAATTTACTC

  7. FINAL RESULT Gypsy, WHAM SOLO LTR, Copia, WIS TIR, Mutator, Annie

  8. 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

  9. Hwk5 – Problem 5 – Complete Annotation

  10. FINAL RESULT

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