This module uses the
repe program to identify and mark known repetitive
elements within the sequences. An example usage is to tag all ALU fragments.
This information may be used by the gap4 assembly algorithm to improve the
assembly by initially ignoring matches between two ALU fragments which may
otherwise produce incorrect assemblies. If available, we recommend using
RepeatMasker instead of this module.
- Option: Repeat file name
This is the filename of a file of filenames, each of which contain a single
repeat to search for. The format of these individual files is plain text
consisting of just the nucleotides and white space.
- Option: Repeat score
This is the minimum score for classifying a matched segment as a repeat.
- Option: Tag type
This is the gap4 tag type to use for identifying this repeat segment. It is
not possible to choose different tag types for different repeats, although the
tag comments contain the match score and match filename.
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Last generated on 22 October 2002.