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Old 03-16-2016, 11:09 AM   #1
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Location: MA

Join Date: Oct 2010
Posts: 160
Default Find telomeric repeats in reference

It is been a while since I have been working with this issue: search and annotate telomeric (interstitial) repeats in a draft reference genome. We know the sequence type of the repeat, two hexamer sequences whose repeats are from 2 to a few dozens.
I don't know why but the literature on the matter, peer-reviewed and forum like, it's not quite extended as in other bioinformatic challenges. Sometimes you hear, in forum threads, RepeatMasker, RepeatModeler, or even approaches like MISA (for microsatellite detection). Also tried blast. Though when I place my self hands-on with this hexamer repeat detection, the results so far are quite limited; there is always a big portion of potential candidates missing from each output. So I wonder, is anyone willing to provide his/her perspective-experience on a bioinformatic problem like this?
Thanks for your time.
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