P-Clouds And Repeatmasker For Searching Repetitive Elements In Human Genome

Question

[Lds]

Hi all,

does anyone know the rationale of p-clouds to search repetitive elements in human genome? What's the advantages and disadvantages of p-clouds when comparing with the classic consensus tool, RepeatMasker? Thanks in advance.

Linus

Answer 1

[Casey Bergman]

Pclouds is a tool for the discovery of repetitive regions in a genome based on over-represented oligomers. It is a de novo method that only takes the genome of interest as input. It does not use a library of known repeats and therefore cannot annotate repeats into families or higher categories.

In contrast, RepeatMasker is a tool that uses a pre-defined library and sequence similarity searches for the annotation of repeats. It can only finds repeats that are in your library, and cannot find unknown repeats (unless they share a high degree of sequence similarity). However, since you it uses prior information, RepeatMasker can label each hit with meta-data about the repeat - eg. family, class, etc.

[Lds]

Thanks for your reply. But what's the algorithms that p-clouds use? I think such a de novo method should be great time-consuming