Transposable elements

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Transposable elements

Contents 1 CAF1 transposable element annotations 2 Some possible areas to work on 3 People interested in TE analysis 4 Discussion and questions 5 Resources

CAF1 transposable element annotations

• ReAS assembled repeat libraries based on raw sequencing reads were released, together with RepeatMasker result of CAF1 version of assemblies; classification of the repeats by comparison with known D.mel TEs (flybase, v9.4.1) and TE-related peptides (gag, pol, env, reverse transcriptase, ribonuclease h, integrase, and transposases); and the number of copies and depth information of each repeat in the genomes. download ftp. I'm sure there are a few false positive sequences in the assembled repeat libraries. So before we can have more high-quality curated libaries, a good idea is to selectively use the libaries according to what kind of analysis you are doing. If you want to mask as many repeats as possible, you can use the whole libary, but if you want to mask repeats conservatively, you can pick up the subset of repeats which have many copies in the genome or matched with known TEs in D.mel or known TE-related proteins.--Ruiqiang Li et. al

• TE annotations based on multiple alignment insertion signatures by Caspi and Pachter, download here

• Transposable element predictions using PILER-DF, masked CAF1 genome sequence, and CAF1 RepeatRunner annotations were generated by Smith & Edgar et. al. and has been submitted for publication. The supplemental data for this publication can be found here ftp://ftp.dhgp.org/pub/DHGP/PILER-DF. This data is provided for public access, but please contact the authors before using in presentations or publications. This data is subject to change depending on requirements for publication. Upon publication a finalized dataset will be provided.

• Transposable element predictions using BLASTER/tblastx with Repbase Update, PILER-DF library (build by Smith & Edgar et al.), and BDGP TE compilation 9.4.1 are available here

Some possible areas to work on

• build libraries of TEs for the CAF1 assemblies.

• use de novo assembly-based methods (e.g., PILER, RECON)
• use de novo read-based methods (e.g., ReAS?)
• use comparative methods (e.g., Caspi and Pachter 2006).

• annotate TEs in each species using species-specific libraries

• use combined evidence pipeline of Quesneville et al (2005)

• Identify ancestral repeats using coordinate maps (a la Mercator) and D. mel TE annotations.

• measure evolutionary rates of these ancestral repeats -- is there any unexpected behavior, i.e. co-variation of TIRs?

[Note see Talk:Transposable_elements]

People interested in TE analysis

• Casey Bergman
• Robert Bradley
• Anat Caspi
• Ian Holmes
• Patrick O'Grady
• Lior Pachter
• Chris Smith
• Hadi Quesneville
• Ruiqiang Li

Discussion and questions

Question: what is the status of Transposable elements in the CAF1 assemblies? A set of PILER-DF de novo TE predictions and complete masked genome sequence have been posted to ftp://ftp.dhgp.org/pub/DHGP/PILER-DF

Mate pairs that are over 3 standard deviations apart have reportedly been crunched down -- is this correct?

One possible effect of this is that tandem arrays of TEs may been collapsed (or removed). What are the implications of this for TE annotation?

Resources

A manually curated dataset of Drosophila melanogaster TE sequences can be found [here].

[Note see Talk:Transposable_elements]