Difference between revisions of "Tutorial"

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(Target/Template alignment)
(Target/Template alignment)
Line 10: Line 10:
 
* Profile to profile
 
* Profile to profile
  
Algorithm:
+
 
 +
Alignment algorithm:
  
 
* Local
 
* Local
 
* Global
 
* Global
 
* Freeshift
 
* Freeshift
 +
 +
 +
Blosum substitution matrix:
 +
 +
#62
 +
#45
 +
#50
 +
#80
 +
  
 
Weighting scheme (only for profiles):
 
Weighting scheme (only for profiles):
Line 21: Line 31:
 
* Henikoff (Henikoff & Henikoff, 1994)
 
* Henikoff (Henikoff & Henikoff, 1994)
 
* SecDivergence (Rychlewski et al., 2000)
 
* SecDivergence (Rychlewski et al., 2000)
 +
  
 
Scoring function (only for profile to profile alignments):
 
Scoring function (only for profile to profile alignments):
Line 37: Line 48:
 
** AtchleyCorrelation  
 
** AtchleyCorrelation  
  
Blosum substitution matrix:
 
  
#62
 
#45
 
#50
 
#80
 
  
  

Revision as of 14:48, 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


Alignment algorithm:

  • Local
  • Global
  • Freeshift


Blosum substitution matrix:

  1. 62
  2. 45
  3. 50
  4. 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
  • Dot product
    • DotPFreq
    • DotPOdds
  • EDistance (Euclidean distance)
  • Pearson
  • JensenShannon
  • Atchley metric
    • AtchleyDistance
    • AtchleyCorrelation




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