Difference between revisions of "Tutorial"

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(Target/Template alignment)
(Target/Template alignment)
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==Target/Template alignment==
 
  
Supposing you have already found a template candidate, you need to align it against your target sequence.
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In the '''sample''' folder are available all input and output files used in this tutorial.  
The '''subali''' application let you choose from very different type of algorithms, strategies and parameters.
+
  
Strategy:
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==Target/Template alignment==
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* Sequence to sequence
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* Profile to sequence
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* Profile to profile
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 +
Supposing you have already found a template candidate, you need to align it against your target sequence. In this dummy example we take the sequences of two homologous proteins both endowed with 3D structure. That allow us to compare different type of alignments to the exact one derived from the structural alignment.
  
Alignment algorithm:
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The two proteins are:
  
* Local
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* Target = 2ANL (chain A)
* Global
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* Template = 1DP5 (chain A)
* Freeshift
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 +
This is the structural alignment:
 +
  
Blosum substitution matrix:
 
  
* 62
 
* 45
 
* 50
 
* 80
 
  
  
Weighting scheme (only for profiles):
+
The '''subali''' application let you choose from very different type of algorithms, strategies and parameters.
 +
 
  
* PSIC (Sunyaev et al., 1999)
 
* Henikoff (Henikoff & Henikoff, 1994)
 
* SecDivergence (Rychlewski et al., 2000)
 
  
  
Scoring function (only for profile to profile alignments):
+
For testing purpose,
  
* Sum of pairs
 
** CrossProduct
 
** LogAverage (Ohsen and Zimmer, 2003; von Ohsen et al., 2003)
 
* Dot product
 
** DotPFreq (Wang and Dunbrack, 2004)
 
** DotPOdds (Wang and Dunbrack, 2004)
 
* EDistance (Euclidean distance)
 
* Pearson (Pietrokovski, 1996)
 
* JensenShannon (Yona and Levitt, 2002)
 
* Atchley metric
 
** AtchleyDistance (Atchley et al., 2005)
 
** AtchleyCorrelation (Atchley et al., 2005)
 
  
  

Revision as of 11:36, 20 August 2014

In the sample folder are available all input and output files used in this tutorial.

Target/Template alignment

Supposing you have already found a template candidate, you need to align it against your target sequence. In this dummy example we take the sequences of two homologous proteins both endowed with 3D structure. That allow us to compare different type of alignments to the exact one derived from the structural alignment.

The two proteins are:

  • Target = 2ANL (chain A)
  • Template = 1DP5 (chain A)

This is the structural alignment:



The subali application let you choose from very different type of algorithms, strategies and parameters.



For testing purpose,




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