What program to use for reference alignment of sequences of very different lengths?

kajsa

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What program to use for reference alignment of sequences of very different lengths?

03-15-2016, 12:53 AM

Hi all,

I have used REPET to find transposable elements (TEs) in a genome and now I want to align the TE-copies to the TE-consensus they come from. The TE-consensuses are often 10 000-15 000 bp long and the TE-copies are between 50-2000 bp long. So very different lengths and very different in divergence also (60-99% identity).

What proper reference assembly/alignment program would you use to do that?

Thank you for your answers!
Kajsa

Last edited by kajsa; 03-15-2016, 05:11 AM.
Tags: different lenghts, reference assembly

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What program to use for reference alignment of sequences of very different lengths?

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