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Tag Repeats

Filename
tag_repeats.p4m

Description
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. 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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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap4_24.html