Difference between revisions of "Tutorial"

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Line 6: Line 6:
#sequence to sequence
#Sequence to sequence
#profile to sequence
#Profile to sequence
#profile to profile
#Profile to profile
Weighting scheme:
Weighting scheme:

Revision as of 12:22, 19 August 2014

Target/Template alignment

Suppose 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.


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


  1. Local
  2. Global
  3. Freeshift

Weighting scheme:

  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:


For more detail use the option -h with the subali application or see the AlignTest code.

Build loops

Evaluate a model