Difference between revisions of "Tutorial"

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(Target/Template alignment)
(Target/Template alignment)
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==Target/Template alignment==
 
==Target/Template alignment==
  
Supposing you have already found a good template, now you need to align it against your target sequence.  
+
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.
 
The '''subali''' application let you choose from very different type of algorithms, strategies and parameters.
  

Revision as of 14:49, 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:

  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