De novo Identification method of LTR Retrotransposon

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De novo Identification method of LTR
Retrotransposon

• Mina Rho

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Contents

• Background
• Algorithm for identification
• Results of cluster and LTRs
• Analysis of similarity, phylogenetic tree, and
  distribution in chromosome

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Background (1)

• LTR retrotransposon
• One of mobile elements which is inserted into
  chromosome.
• They copy themselves into RNA and back to DNA by
  reverse transcriptase.

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Long Terminal Repeat (LTR)
Identity gt 80
100 bp 2000 bp
100 bp 2000 bp
RT
RNaseH
IN
1000bp 20000 bp
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Full-length and Solo LTRs
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Background (2)

• Information of evolution, mutation, changes of
  amount of DNA in the genome.
• No need to the existing libraries for homology
  search

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LTR Retrotransposons
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Algorithm (1)

• Identification of full-length LTR

1)
2)
100bp
3)
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Algorithm (2)

• Identification of solo LTRs
• Cluster Full-length LTRs by BAG
• Build HMM for each cluster by HMMBuild
• Search solo LTRs against HMM by HMMSearch

HMM1
HMM2
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Algorithm (3)

• Identification of additional full-length LTR
• Build phylogenetic tree of LTRs in each cluster
  by ClustalW

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Results

• New elements and clusters

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Analysis (1)

• Distribution of LTRs
• Kolmogorov-Smirnov test (H0 Uniform
  distribution)
• C.elegans
• Chr I,II, V, X Accepted
• Chr III, IV Rejected (p0.4586 and P0.1420)
• D.melanogaster
• Chr II, III, IV, X Rejected

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Chromosomal position of LTRs (C.elegans)
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Distribution of LTRs (D.melanogaster)
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Analysis (2)

• Phylogenetic tree of RT

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