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!
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!
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