Difference between revisions of "Tandem Repeat Concepts"

From Genome Analysis Wiki
Jump to: navigation, search
(Algorithm for Detection)
(Classification)
Line 6: Line 6:
  
 
A series of repeats that are contiguous
 
A series of repeats that are contiguous
 +
 +
 +
= Concepts =
 +
 +
== Motif Canonical Class ==
 +
 +
=== Shifting ===
 +
 +
=== Reverse Complement ===
 +
 +
== Acyclicity  ==
 +
 +
 +
== Fractional counts  ==
 +
 +
== Scoring  ==
 +
 +
== TRF Scoring  ==
 +
 +
== Normalized scoring  ==
 +
 +
  
 
= Classification =  
 
= Classification =  
Line 13: Line 35:
 
* repeat tract lengfth
 
* repeat tract lengfth
 
* purity
 
* purity
 +
  
 
== Algorithm for Detection ==
 
== Algorithm for Detection ==

Revision as of 20:35, 12 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

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.