Difference between revisions of "Tutorial"

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(Target/Template alignment)
(Target/Template alignment)
Line 6: Line 6:
 
Strategy:
 
Strategy:
 
   
 
   
#Sequence to sequence
+
* Sequence to sequence
#Profile to sequence
+
* Profile to sequence
#Profile to profile
+
* Profile to profile
  
 
Algorithm:
 
Algorithm:
  
#Local
+
* Local
#Global
+
* Global
#Freeshift
+
* Freeshift
  
 
Weighting scheme (only for profiles):
 
Weighting scheme (only for profiles):
  
#PSIC
+
* PSIC (Sunyaev et al., 1999)
#Henikoff
+
* Henikoff (Henikoff & Henikoff, 1994)
#SecDivergence
+
* SecDivergence (Rychlewski et al., 2000)
  
 
Scoring function:
 
Scoring function:
  
#CrossProduct  
+
* CrossProduct  
#LogAverage  
+
* LogAverage  
#DotPFreq  
+
* DotPFreq  
#DotPOdds  
+
* DotPOdds  
#EDistance  
+
* EDistance  
#Pearson  
+
* Pearson  
#JensenShannon  
+
* JensenShannon  
#AtchleyDistance  
+
* AtchleyDistance  
#AtchleyCorrelation  
+
* AtchleyCorrelation  
  
 
Blosum substitution matrix:
 
Blosum substitution matrix:

Revision as of 14:44, 19 August 2014

Target/Template alignment

Supposing you have already found a good template, now you need to align it against your target sequence. The subali application let you choose from very different type of algorithms, strategies and parameters.

Strategy:

  • Sequence to sequence
  • Profile to sequence
  • Profile to profile

Algorithm:

  • Local
  • Global
  • Freeshift

Weighting scheme (only for profiles):

  • PSIC (Sunyaev et al., 1999)
  • Henikoff (Henikoff & Henikoff, 1994)
  • SecDivergence (Rychlewski et al., 2000)

Scoring function:

  • CrossProduct
  • LogAverage
  • DotPFreq
  • DotPOdds
  • EDistance
  • Pearson
  • JensenShannon
  • AtchleyDistance
  • AtchleyCorrelation

Blosum substitution matrix:

  1. 62
  2. 45
  3. 50
  4. 80



The fist step is to put the target and the template fasta sequences in a single file like that:

>target
VLEEIAKDHGEALTI....
>template
AFQVTSIPTLILFQ....


For more detail use the option -h with the subali application or see the AlignTest code.

Build loops

Evaluate a model