Transposable Elements (TE) in genomic sequence . Mina Rho. Contents. Definition De novo identification of repeat families in large genomes (RepeatScout) Alkes L. Price, Neil C. Jones and Pavel A. Pevzner Combined Evidence Annotation of Transposable Elements in Genome Sequences
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Alkes L. Price, Neil C. Jones and Pavel A. Pevzner
Hadi Quesneville, Casey M. Bergman, Olivier Andrieu, Delphine Autard, Danielle Nouaud, Michael Ashburner, Dominique Anxolabehere
- a segment of DNA that can move around to different positions in the genome of a single cell.
- cut out of its location and inserted into a new location.
- consisting of DNA.
- copy and paste into a new location.
- the copy is made of RNA and transcribed back into DNA using reverse transcriptase.
- long terminal repeats (LTRs) at its ends.
=> expect to get information of evolution, mutation, changes of amount of DNA in the genome.
Position of last occurrence
AAAAAAAAAAAGATA 8 2920943
AAAAAAAGGAAAGAA 5 2468525
AGGCTTGAACAATGG 3 1425014
AAAAAAAAGAAAGAA 62 3009663
GTTGGTTTCAAAGAA 7 2855871
AAAAAAAATTTTTTT 22 2992836
ATTCAAGTTAAATGG 4 1473342
ATTCAATGTAACCAC 3 1463008
ATGCATGCAATGCAT 9 1788944
ATGCATTTAAAAGAA 3 1464381
AAAAAACTCACTCCA 5 1489159
High frequency l-mer
Query sequence (with l-mer1)
Extending Q maximizing
objective function one nucleotide
at a time
|Q| : the length of Q
C: minimum threshold on the number of repeat elements
a(Q, Sk): a pairwise fit_preferred alignment score
p: Incomplete-fit penalty
Query Sequences: Drosophila melanogaster (Fruit fly) Release 3, 4
Combined evidence model: pipeline of RepeatMasker, BLASTER, TBLASTX, all-by-all BLASTN, RECON, and TE-HMM
- Methods for the annotation of known TE families
- Methods for the annotation of anonymous TE families
Benchmark : FlyBase Release 3.1 annotation
Sensitivity and specificity, characteristics of boundary
For each nucleotide,