What's the meaning and difference of Target and Class in the gff result of RepeatMasker?

Question

[comma1993]

ID=TE0000001;Target=lcl|DIRS-1F-LTR_DR 185 214;Class=LTR/Ngaro;PercDiv=22.8;PercDel=6.2;PercIns=1.6;

What's the meaning and difference of Target and Class in the gff result of RepeatMasker? I want to build phylogenetic trees but I don't know which information to use.

Answer 1

[lieven.sterck]

Target points to the specific instance of a repeat, while class denotes the general classification the repeat belongs to . In this case the repeat is part of the LTR/Ngaro types of repeats. These classes can have several copies (== targets) in the genome.

For phylogenetic purposes it depends a little how detailed you want to go. Normally all instances of the same class should end up together in the tree.

[comma1993]

Thanks very much! It helps a lot !