annotating retroelements dotter, identify direct and inverted repeats, and graphically visualize...
Post on 20-Dec-2015
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![Page 1: Annotating Retroelements Dotter, identify direct and inverted repeats, and graphically visualize them. (Rough idea of coordinates – highlight in your sequence,](https://reader031.vdocuments.site/reader031/viewer/2022032704/56649d445503460f94a20850/html5/thumbnails/1.jpg)
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).
![Page 2: Annotating Retroelements Dotter, identify direct and inverted repeats, and graphically visualize them. (Rough idea of coordinates – highlight in your sequence,](https://reader031.vdocuments.site/reader031/viewer/2022032704/56649d445503460f94a20850/html5/thumbnails/2.jpg)
LTR Retroelement
LTR
SHORT INVERTED REPEATS FLANK LTRHOST REPEATS
![Page 3: Annotating Retroelements Dotter, identify direct and inverted repeats, and graphically visualize them. (Rough idea of coordinates – highlight in your sequence,](https://reader031.vdocuments.site/reader031/viewer/2022032704/56649d445503460f94a20850/html5/thumbnails/3.jpg)
LTR Retroelement
![Page 4: Annotating Retroelements Dotter, identify direct and inverted repeats, and graphically visualize them. (Rough idea of coordinates – highlight in your sequence,](https://reader031.vdocuments.site/reader031/viewer/2022032704/56649d445503460f94a20850/html5/thumbnails/4.jpg)
TIRs
GAGTAAAATGCAAGAAACCCACTTTGAAGGCTAGGTTTGCAGATAACACTACGTTACATTTTTTGGACAGAAAGCACCACGTCTCGTGTAATCTTGTTGCAAATAACACTGATTGGCGGATTAGAGCGCTTAAAGTATGTTTATGACAGGAGGGTCCAGATTTTGCCCTTGTGGCGTAACGGCTTGGCCATGACGGCGT------>
<------ACGCCGTTTCGCCCCAAGCCGTTATGTCACATGGGCAAAATCTGGAACCACCTGTCATAAACACACTTAAAGCACTCTAATCCGCCAATCAGTGTTATTTGCAATAAGATTACACAAAACGTGATGCTTTTTGTTCAAAAAATGTAACGTAGTGTTATCTGCAAACCTAGCCTTCAAAATGGTGGTTTTATGCAATTTACTC
Reverse complement
![Page 5: Annotating Retroelements Dotter, identify direct and inverted repeats, and graphically visualize them. (Rough idea of coordinates – highlight in your sequence,](https://reader031.vdocuments.site/reader031/viewer/2022032704/56649d445503460f94a20850/html5/thumbnails/5.jpg)
SOLO LTRs
LTR
SHORT INVERTED REPEATS FLANK LTRHOST REPEATS
![Page 6: Annotating Retroelements Dotter, identify direct and inverted repeats, and graphically visualize them. (Rough idea of coordinates – highlight in your sequence,](https://reader031.vdocuments.site/reader031/viewer/2022032704/56649d445503460f94a20850/html5/thumbnails/6.jpg)
Example Retroelement Annotation
![Page 7: Annotating Retroelements Dotter, identify direct and inverted repeats, and graphically visualize them. (Rough idea of coordinates – highlight in your sequence,](https://reader031.vdocuments.site/reader031/viewer/2022032704/56649d445503460f94a20850/html5/thumbnails/7.jpg)
FINAL RESULT
Gypsy, WHAM
TIR, Mutator, Annie
SOLO LTR, Copia, WIS
![Page 8: Annotating Retroelements Dotter, identify direct and inverted repeats, and graphically visualize them. (Rough idea of coordinates – highlight in your sequence,](https://reader031.vdocuments.site/reader031/viewer/2022032704/56649d445503460f94a20850/html5/thumbnails/8.jpg)
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
![Page 9: Annotating Retroelements Dotter, identify direct and inverted repeats, and graphically visualize them. (Rough idea of coordinates – highlight in your sequence,](https://reader031.vdocuments.site/reader031/viewer/2022032704/56649d445503460f94a20850/html5/thumbnails/9.jpg)
Complete Annotation – Identify Retros
![Page 10: Annotating Retroelements Dotter, identify direct and inverted repeats, and graphically visualize them. (Rough idea of coordinates – highlight in your sequence,](https://reader031.vdocuments.site/reader031/viewer/2022032704/56649d445503460f94a20850/html5/thumbnails/10.jpg)
Complete Annotation – Identify Genes
![Page 11: Annotating Retroelements Dotter, identify direct and inverted repeats, and graphically visualize them. (Rough idea of coordinates – highlight in your sequence,](https://reader031.vdocuments.site/reader031/viewer/2022032704/56649d445503460f94a20850/html5/thumbnails/11.jpg)
FINAL RESULT