Genome masking
From CoGepedia
CoGe masks genomes by using NCBI's windowmasker: http://www.ncbi.nlm.nih.gov/pubmed/16287941
Currently, our pipeline for masking is:
- Generate frequency counts for the masking database for the genome
- windowmasker -in <genome> -mk_counts -out <counts>
- Mask genome
- windowmasker -in <genome> -ustat <counts> -outfmt fasta -dust T -out <masked genome>
- Convert soft masking (lower case sequence data) to "X".
- CoGe's visualizations often use purple to represent genome sequence "X" to make the identification of masked reasons easy
For users that are logged in, CoGe provides an option to mask a genome through GenomeInfo
