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Repeat definitions

The repeat definition files are BED files containing repeat coordinates and information about the repeat structure. The first three columns specify the coordinates of the repeat region. The fourth column contains the following mandatory fields:

  • Repeat identifier (ID). The identifier must be globally unique.
  • The comma-separated list of repeat motifs (MOTIFS) specifying all possible motifs that can appear in this region. In particular, each motif present in the STRUC field must also be present in this field.
  • Repeat region structure (STRUC). This field describes the overall structure of the repeat region. It is composed of one or more tandem repeats, each defined by the expression (<motif>)n. Tandem repeats can optionally separated by interrupting sequences. See the example below.

For example, consider this definition of tandem repeat:

chr4  3074876  3074966  ID=HTT,MOTIFS=CAG,CCG;STRUC=(CAG)nCAACAG(CCG)n

This definition tells us that the repeat region has coordinates chr4:3074876-3074966. Its identifier is HTT. The region contains two tandem repeats with motifs CAG and CCG and these tandem repeats are expected to be separated by a short interrupting sequence CAACAG.