# Difference between revisions of "Tandem Repeat Concepts"

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== Acyclicity == | == 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. | ||

== Fractional counts == | == Fractional counts == |

## Revision as of 18:48, 25 February 2016

# Introduction

This page is about Tandem Repeats.

# Definition

A series of repeats that are contiguous

# Concepts

## Motif Canonical Class

### Shifting

### Reverse Complement

## 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.

## Fractional counts

## Scoring

## TRF Scoring

## Normalized scoring

# Classification

- motif length
- motif basis
- repeat tract lengfth
- purity

## Algorithm for Detection

## Detection of a motif in a sequence

## Model free left alignment and right alignment

## Model based fuzzy left alignment and right alignment

## Model free fuzzy left alignment and right alignment

# Implementation

This is implemented in vt.

# Citation

# Maintained by

This page is maintained by Adrian.