Difference between revisions of "Tutorial"

From victor
Jump to: navigation, search
Line 1: Line 1:
 
==Target/Template alignment==
 
==Target/Template alignment==
  
To initiate the alignment process you need to put the target and the template fasta sequences in a file, that will be the input file for the application.
+
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:
 +
 
 
  >target
 
  >target
 
  VLEEIAKDHGEALTI....
 
  VLEEIAKDHGEALTI....
Line 7: Line 8:
 
  AFQVTSIPTLILFQ....
 
  AFQVTSIPTLILFQ....
  
Then depending of what type of alignment you want, you can choose between  
+
 
  sequence to sequence
+
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:
profile to sequence
+
   
profile to profile
+
#sequence to sequence
 +
#profile to sequence
 +
#profile to profile
  
 
Also you can choose between the alignment algorithm to use
 
Also you can choose between the alignment algorithm to use

Revision as of 11:18, 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 fist step is to put the target and the template fasta sequences in a single file like that:

>target
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:

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

Also you can choose between the alignment algorithm to use

local
global
freeshift

if you choose profile to sequence or profile to profile type you can decide to use a specific Weighting scheme

PSIC
Henikoff
SecDivergence

And also choose a scoring function

CrossProduct 
LogAverage 
DotPFreq 
DotPOdds 
EDistance 
Pearson 
JensenShannon 
AtchleyDistance 
AtchleyCorrelation 

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.

Build loops

Evaluate a model