Difference between revisions of "Tutorial"

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==Target/Template alignment==
 
==Target/Template alignment==
  
Suppose you have already found a good template, now you need to align it against your target sequence. The fist step is to put the target and the template fasta sequences in a single file like that:
+
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.
  
>target
+
Strategy:
VLEEIAKDHGEALTI....
+
>template
+
AFQVTSIPTLILFQ....
+
 
+
 
+
Now you can choose from very different type of algorithms, strategies and parameters.Then depending of what type of alignment you want, you can choose between:
+
 
   
 
   
 
#sequence to sequence
 
#sequence to sequence
Line 15: Line 10:
 
#profile to profile
 
#profile to profile
  
Also you can choose between the alignment algorithm to use
+
Algorithm:
local
+
global
+
freeshift
+
  
if you choose profile to sequence or profile to profile type you can decide to use a specific Weighting scheme
+
#local
PSIC
+
#global
Henikoff
+
#freeshift
SecDivergence
+
  
And also choose a scoring function
+
Weighting scheme:
CrossProduct  
+
 
LogAverage  
+
#PSIC
DotPFreq  
+
#Henikoff
DotPOdds  
+
#SecDivergence
EDistance  
+
 
Pearson  
+
Scoring function:
JensenShannon  
+
 
AtchleyDistance  
+
#CrossProduct  
AtchleyCorrelation  
+
#LogAverage  
 +
#DotPFreq  
 +
#DotPOdds  
 +
#EDistance  
 +
#Pearson  
 +
#JensenShannon  
 +
#AtchleyDistance  
 +
#AtchleyCorrelation  
 +
 
 +
Blosum substitution matrix:
 +
 
 +
#62
 +
#45
 +
#50
 +
#80
 +
 
 +
 
 +
 
 +
 
 +
The fist step is to put the target and the template fasta sequences in a single file like that:
 +
 
 +
>target
 +
VLEEIAKDHGEALTI....
 +
>template
 +
AFQVTSIPTLILFQ....
  
With all the alignment types you can decide to use a blosum substitution matrix of 62, 45, 50 or 80.
 
  
 
For more detail use the option -h with the subali application or see the [[AlignTest]] code.
 
For more detail use the option -h with the subali application or see the [[AlignTest]] code.

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.

Strategy:

  1. sequence to sequence
  2. profile to sequence
  3. profile to profile

Algorithm:

  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:

>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