When is repeat masking necessary?

[EricSchon]

Hi all

I am planning to work on some comparative genomics where I look at secondary metabolite biosynthetic genes in multiple species of the same genus. I am planning fetch the genomes from jgi, but I am not sure wether I should use the masked or unmasked versions.

The software tools I am planning to use do alignments and apply HMMs to the genome. I will probably also do other comparative analysis later so I wonder:

- For my purpose doing alignments/HMMs is masked or unmasked better?
- Is it possible to say in general for which kind of analysis masked/unmasked genomes are better? When is it important to be aware of which one to use?

Thanks!

[Brian Bushnell]

I recommend strictly avoiding the masked genomes. I do not think repeat masking is ever necessary. And particularly, there's no description of exactly how or why the genomes were masked, which makes it doubly important to avoid the masked versions.

Incidentally, I work at JGI