RepeatMasker is not included as part of the Staden Package. It is available
from Arian Smit.
This module uses the
RepeatMasker program. This is a program which
searches for a comprehensive set of repeat sequences. Any matches which are
found will be tagged with a comment indicating the type of repeat. These tags
will then be visible from within gap4. Full documentation is available from
the author of RepeatMasker, or from typing
- Option: Repeat library
This specifies the directory containing the library of repeat sequences. Only
one library directory may be specified. The library "<default>" will let
RepeatMasker use its own default library.
- Option: RepeatMasker cutoff
This specifies the cutoff score for RepeatMasker. The documentation with
RepeatMasker states that a cutoff of 250 will guarantee no false positives.
- Option: Gap4 tag type
When a repeat is found a tag will be added to the Experiment File. This
specifies the tag type to use. It should be one of the tag types available to
Gap4, but other tag types may be used if desired (they will be coloured as is
COMMent tags in gap4).
- Option: Types of repeat to screen against
The default setting of RepeatMasker is to search for primate repeats, however
it may be told to search for other repeat families or to restrict its search
to only ALU primate repeats. The full list of options here are Alu only,
Rodent only, Simple only, Mammalian excluding primate/rodent, and no low
complexity. These are as defined in the RepeatMasker documentation. It is not
known what effect enabling mutually exclusive options will have.
This page is maintained by
Last generated on 22 October 2002.