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#1
06-01-2011, 09:10 PM
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 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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#2
06-02-2011, 09:10 AM
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 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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#3
06-03-2011, 10:56 AM
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| 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. |
| The Following User Says Thank You to mfursov For This Useful Post: | ||
lxyouc (06-04-2011)
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| find , genome , tes |
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