Difference between revisions of "Tutorial"

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(Target/Template alignment)
(Target/Template alignment)
Line 22: Line 22:
 
* SecDivergence (Rychlewski et al., 2000)
 
* SecDivergence (Rychlewski et al., 2000)
  
Scoring function:
+
Scoring function (only for profile to profile alignments):
  
 
* Sum of pairs
 
* Sum of pairs

Revision as of 13:47, 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 (only for profile to profile alignments):

  • Sum of pairs
    • CrossProduct
    • LogAverage
  • Dot product
    • DotPFreq
    • DotPOdds
  • EDistance (Euclidean distance)
  • Pearson
  • JensenShannon
  • Atchley metric
    • 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