Maybe this is NOT a bioinformatic question. But I bet many people here may deal with such genomic concepts, so I wanna ask this.
So what's the relationship between the two? Difference is SD is much larger than TE and low in copy number? And TE actually causes SD?
I'm always confused by the two.
thx
Segmental duplications are pieces of otherwise unique (or low copy number) genomic DNA that become duplicated at dispersed or tandem sites in the genome. The sequences involved in SDs do not directly encode the information for their duplication.
Transposable elements are mobile genomic DNA sequences that encode information for their duplicative replication, either through DNA based (transposons) or RNA based (retrotransposons) mechanisms.
The difference is not in copy number or length but in the molecular mechanism of formation. You are correct in saying that TE activity can cause TEs, via a range of mechanisms. For a good discussion see: http://www.ncbi.nlm.nih.gov/pubmed/17726166
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Just to add a bit to this, segmental duplications can arise by ectopic recombination (aka non-allelic homologous recombination; NAHR) between nearby, highly similar, TEs on the the same chromosome.
thx...but how can people then distinguish SD from TE only based on read-depth(say in those whole-genome scale identification of SD)? Read-depth for both SD and TE are increased compared with unique regions...
@bioscientist - Yes, this is true. Classification of a sequence as a TE or SD based on read depth is not rigorous. However in general active TEs should present orders of magnitude higher read depth than the unique regions of the genome or SDs.