Genome masking

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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

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