What are rnd families predicted by RepeatModeler?
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11 weeks ago

Hi,

I am working with transposon and repeated-sequences prediction in some non-model oomycetes. I used RepeatModeler and the majority of the detected families are classified as rnd-something (example: rnd-1_family-8). I am new to transposon analysis and I cannot really find much information on what these rnd families are. Can someone suggest me a way on how to interpret this type of classification? Should I use another program to classify transposons?

Repeats Transposons RepeatModeler oomycetes • 276 views
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I have the same problem, did you find any solution?

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I've also been looking at this. From what I gather, if you use the -LTRStruct option in RepeatModeler which enables the optional LTR structural finder introduced in RepeatModeler2, you will get two sources of repeats - those from the LTR structural finder, called for example 'ltr-1_family-10', and those from RepeatScout or RECON, called for example 'rnd-1_family-10'. If you look at the [genome]-families.fa file produced by RepeatModeler2, you'll see something like this:

>ltr-1_family-9#LTR/Gypsy [ Type=INT, Final Multiple Alignment Size = 3 ]
>ltr-1_family-10#LTR/Gypsy [ Type=INT, Final Multiple Alignment Size = 4 ]
>rnd-1_family-3#LTR/Gypsy ( RepeatScout Family Size = 1353, Final Multiple Alignment Size = 100, Localized to 14 out of 17 contigs )
>rnd-1_family-2#LTR/Gypsy ( RepeatScout Family Size = 1472, Final Multiple Alignment Size = 100, Localized to 14 out of 17 contigs )
>rnd-3_family-264#LTR/Gypsy ( Recon Family Size = 19, Final Multiple Alignment Size = 19 )