Difference between revisions of "Tutorial"

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(Target/Template alignment)
(Target/Template alignment)
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==Target/Template alignment==
 
==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.
+
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 allows us to compare different type of Victor alignments with the "exact" one derived from the structural alignment.
  
 
The two proteins are:
 
The two proteins are:
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* Template = 1DP5 (chain A)
 
* Template = 1DP5 (chain A)
  
 
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They superimpose quite well (RMSD 2.03 A) considering the low level of sequence identity (28.06%). This is the resulting sequence alignment after superimposing the two structures:
This is the alignment resulting by superimposing the two structures:
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[[File:3d_align.png|700px]]
 
[[File:3d_align.png|700px]]
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[[File:alignment_cartoon.png|300px|left]]
 
[[File:alignment_cartoon.png|300px|left]]
 
[[File:alignment_ribbon.png|300px|rigth]]
 
[[File:alignment_ribbon.png|300px|rigth]]
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Revision as of 10:56, 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 allows us to compare different type of Victor alignments with the "exact" one derived from the structural alignment.

The two proteins are:

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

They superimpose quite well (RMSD 2.03 A) considering the low level of sequence identity (28.06%). This is the resulting sequence alignment after superimposing the two structures:

3d align.png

Alignment cartoon.png

rigth


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