Tandem Repeat Concepts - Revision history

Atks: /* Detection of a motif in a sequence */

2016-02-25T23:17:38Z

Detection of a motif in a sequence

2016-02-25T23:16:40Z

Introduction

← Older revision		Revision as of 19:16, 25 February 2016
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	This wiki is an attempt at consolidation on past work by many people		This wiki is an attempt at consolidation on past work by many people

			We talk about its representation, major characteristics, and a set of useful definitions and algorithms for working with them

	* Gary Benson's tandem repeat finder's		* Gary Benson's tandem repeat finder's

2016-02-25T23:15:37Z

Introduction

← Older revision		Revision as of 19:15, 25 February 2016
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	Tandem repeats are a common polymorphism in the genome.		Tandem repeats are a common polymorphism in the genome.

	This wiki ~~talks about its representation - and compiles from previous~~ work ~~-especially~~ by Gary Benson's tandem repeat finder's ~~output~~.		This wiki is an attempt at consolidation on past work by many people


			* Gary Benson's tandem repeat finder's
			* Gymrek et al.
			* Highnam et al.

	= Definition =		= Definition =

2016-02-25T23:14:25Z

Classification

← Older revision		Revision as of 19:14, 25 February 2016
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	GAAAGAAGGAAAAGAGAGAAAAGAAGAAGAA		GAAAGAAGGAAAAGAGAGAAAAGAAGAAGAA

	= ~~Classification~~ =		= Characteristics =

	* motif length		* motif length
	* motif basis		* motif basis
	* repeat tract ~~lengfth~~		* repeat tract length
	* purity		* purity

			questions.

			Is AAAAC really different from AAAAAC?

2016-02-25T23:13:19Z

Normalized scoring

← Older revision		Revision as of 19:13, 25 February 2016
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	A nice useful scheme is +2 for matches and -7 for indels and mismatches, and it provides a convenient way of scoring for purity.		A nice useful scheme is +2 for matches and -7 for indels and mismatches, and it provides a convenient way of scoring for purity.

	== ~~Normalized scoring~~ ==		== Inexact Tandem Repeats ==

			We see alot of this

			AAAAAAAAAAAGAAAAAAAAAAAAAA

			or

			ACACACACACACGACACACAACACACACACAC

			or

			GAAAGAAGGAAAAGAGAGAAAAGAAGAAGAA

	= Classification =		= Classification =

2016-02-25T23:12:13Z

Introduction

← Older revision		Revision as of 19:12, 25 February 2016
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	= Introduction =		= Introduction =

	This ~~page is~~ about ~~Tandem Repeats~~.		Tandem repeats are a common polymorphism in the genome.

			This wiki talks about its representation - and compiles from previous work -especially by Gary Benson's tandem repeat finder's output.

	= Definition =		= Definition =

2016-02-25T23:09:53Z

Scoring

← Older revision		Revision as of 19:09, 25 February 2016
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	== Scoring ==		== Scoring ==

			You can use a score bounded by one.

			By random matching -

	== TRF Scoring ==		== TRF Scoring ==

2016-02-25T23:08:28Z

Algorithm for Detection

← Older revision		Revision as of 19:08, 25 February 2016
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	== Algorithm for Detection ==		== Algorithm for Detection ==

			Exact alignment algorithm

			Fuzzy alignment algorithm

	== Detection of a motif in a sequence ==		== Detection of a motif in a sequence ==

2016-02-25T23:08:10Z

TRF Scoring

← Older revision		Revision as of 19:08, 25 February 2016
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	== TRF Scoring ==		== TRF Scoring ==

			A nice useful scheme is +2 for matches and -7 for indels and mismatches, and it provides a convenient way of scoring for purity.

	== Normalized scoring ==		== Normalized scoring ==

2016-02-25T23:07:09Z

Motif Canonical Class

← Older revision		Revision as of 19:07, 25 February 2016
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	== Motif Canonical Class ==		== Motif Canonical Class ==

			Using the concepts of shifting, the canonical class of a set of motifs can be defined as
			a equivalence relationship.

			ACG ~ CGA if there exists a shift that allows s(ACG, i) = CGA

			This relationship can be show to be reflexive, symmetric and transitive. And a equivalence
			class can be defined on this.

			Example:

			This is a distribution of motifs without collapsing

			A
			C
			G
			T
			AA
			CC
			GG
			TT
			AC
			AG
			AT
			CG
			CT
			GT
			CA
			GA

			show all permutations
			show acyclic
			show shift
			show reverse complement





	=== Shifting ===		=== Shifting ===