RepeatMasker

Filename

tag_repeats.p4m

Description

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 RepeatMasker -h. RepeatMasker is not included as part of the Staden Package. It is available from Arian Smit.

Smit, A. http://www.genome.washington.edu/UWGC/analysistools/repeatmask.htm.

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.