Difference between revisions of "Tutorial"

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(Target/Template alignment)
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#Freeshift
 
#Freeshift
  
Weighting scheme:
+
Weighting scheme (only for profiles):
  
 
#PSIC
 
#PSIC

Revision as of 14:36, 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:

  1. Sequence to sequence
  2. Profile to sequence
  3. Profile to profile

Algorithm:

  1. Local
  2. Global
  3. Freeshift

Weighting scheme (only for profiles):

  1. PSIC
  2. Henikoff
  3. SecDivergence

Scoring function:

  1. CrossProduct
  2. LogAverage
  3. DotPFreq
  4. DotPOdds
  5. EDistance
  6. Pearson
  7. JensenShannon
  8. AtchleyDistance
  9. 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