[BiO BB] Genome Masking

[FREDERICK TAN]

Good evening,

. Could anyone comment on their experience masking entire genomes?  I'm
interested in trying to mask out general repeats in a genome of
approximately 10^8 bases.  I've noticed that RepeatMasker has libraries
of known repeats for different organisms, but I'm interested in a general
masking.

. I came across one paper in Bioinformatics from Warren Gish's lab
discussing MaskerAid, which supposedly has a 30-fold increase in speed at
the most sensitive setting over the regular RepeatMasker.

. Additionally, since it appears that the RepeatMasker web server at UW
will only accept up to 100kb, a local installation of the software would
be necessary.  

. Thanks in advance!

Sincerely,
Frederick Tan