Difference between revisions of "Tutorial"

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(Target/Template alignment)
(Target/Template alignment)
Line 37: Line 37:
 
* Sum of pairs
 
* Sum of pairs
 
** CrossProduct  
 
** CrossProduct  
** LogAverage
+
** LogAverage (Ohsen and Zimmer, 2003; von Ohsen et al., 2003)
 
* Dot product  
 
* Dot product  
** DotPFreq  
+
** DotPFreq (Wang and Dunbrack, 2004)
** DotPOdds  
+
** DotPOdds (Wang and Dunbrack, 2004)
 
* EDistance (Euclidean distance)  
 
* EDistance (Euclidean distance)  
* Pearson  
+
* Pearson (Pietrokovski, 1996)
* JensenShannon  
+
* JensenShannon (Yona and Levitt, 2002)
 
* Atchley metric
 
* Atchley metric
** AtchleyDistance  
+
** AtchleyDistance (Atchley et al., 2005)
** AtchleyCorrelation  
+
** AtchleyCorrelation (Atchley et al., 2005)
  
  

Revision as of 14:54, 19 August 2014

Target/Template alignment

Supposing you have already found a template candidate, 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


Alignment algorithm:

  • Local
  • Global
  • Freeshift


Blosum substitution matrix:

  • 62
  • 45
  • 50
  • 80


Weighting scheme (only for profiles):

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


Scoring function (only for profile to profile alignments):

  • Sum of pairs
    • CrossProduct
    • LogAverage (Ohsen and Zimmer, 2003; von Ohsen et al., 2003)
  • Dot product
    • DotPFreq (Wang and Dunbrack, 2004)
    • DotPOdds (Wang and Dunbrack, 2004)
  • EDistance (Euclidean distance)
  • Pearson (Pietrokovski, 1996)
  • JensenShannon (Yona and Levitt, 2002)
  • Atchley metric
    • AtchleyDistance (Atchley et al., 2005)
    • AtchleyCorrelation (Atchley et al., 2005)




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