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How to find TEs in a genome, please?

How to find TEs in a genome, please? - Bioinformatics

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Old 06-01-2011, 09:10 PM
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Question How to find TEs in a genome, please?



I've got a 454 dataset assembled to ESTs, and now i need to find out all the transposable elements from it. Could anyone help give me some instructions or suggestions on it. Please don't just say something like blast... i'm really a greenhand:P Thank you =)
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Old 06-02-2011, 09:10 AM
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Default Re: How to find TEs in a genome, please?

ok i'll replay myself...
read the papers:
Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs
by E Lerat, 2010
and
Discovering and detecting transposable elements in genome sequences
by Casey M. Bergman and Hadi Quesneville
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Old 06-03-2011, 10:56 AM
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Default Re: How to find TEs in a genome, please?

An option here: try using UGENE Query Designer for genome auto-annotation:

Construct a pattern that represents your TE:

repeats + orf inside + some domains from CDD datatabase (revertase, integrase etc) and run this query on your DNA sequence. All regions that matches your pattern will be shown as groups of sequence annotations.
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