Tandem Repeat Concepts

Introduction

This page is about Tandem Repeats.

Definition

A series of repeats that are contiguous

Concepts

Acyclicity

Motifs are required to be acyclic. For example, a motif ACACAC should just be represented by AC as it is 3 copies of AC.

  A sequence is cyclic if and only if there exists a sub sequence in which it is a multiple copy of.

The definition can be more explicit as follows:

 A sequence is cyclic if and only if there exists a non trivial shift of the sequence that is equivalent to  the sequence.

Take for example, the sequence ACACA, is this a bona fide motif? After it seems like it is 2.5 copies of AC and AC might be more appropriate.

 shift 0: ACACA
 shift 1: CACAA
 shift 2: ACAAC
 shift 3: CAACA
 shift 4: AACAC

So ACACA is a bona fide motif.

Classification

• motif length
• motif basis
• repeat tract lengfth
• purity

Implementation

This is implemented in vt.

Maintained by

This page is maintained by Adrian.