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