Difference between revisions of "Sequence Alignments TSD"

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(cleanup, add protocol link)
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Here some of them are applied for the Hex A protein and analyzed. For the searches non redundant protein databases are used. The outputs are adapted to each other and put in comparison in order to determine the best results. A [[Sequence Alignments Protocol TSD|protocol]] containing the basic steps taken is available.
  
Here some of them are applied for the Hex A protein and analyzed. For the searches non redundant protein databases are used. The outputs are adapted to each other and put in comparison in order to determine the best results. A [[Sequence Alignments Protocol TSD|protocol]] containing the basic steps taken is available.
 
===Blast===
  
===Blast===
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<!-- <figure id="fig:tsd_gm2">
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[[Image:TSD GM2 ganglioside.png|300px|thumb|<caption>TODO</caption>]]
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</figure> -->
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...
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Figure <xr id="fig:Agent_LifeCycle#1"/> illustrates the standard agent's life-cycle.
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...
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Figure <xr id="fig:Agent_LifeCycle#2"/> illustrates the finer agent's life-cyle,
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...
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<figure id="fig:Agent_Life_Cycle">
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<twocolumns>
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<subfigure>
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[[Image:Standard Agent LifeCycle.png|frame|<caption>Standard Agent's Life-Cycle</caption>]]
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</subfigure>
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<break>
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<subfigure>
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[[Image:Finer Agent LifeCycle.png|frame|<caption>Finer Agent's Life-Cycle</caption>]]
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</subfigure>
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</twocolumns>
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<center><small><caption>Life Cycles of Agent</caption></small></center>
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</figure>
   
 
===PSI-Blast===
  
===PSI-Blast===

Revision as of 19:34, 3 May 2012

Sequence searches

There are several alignment methods provided by various initiatives, who tackle the problem of sequence searches. Here some of them are applied for the Hex A protein and analyzed. For the searches non redundant protein databases are used. The outputs are adapted to each other and put in comparison in order to determine the best results. A protocol containing the basic steps taken is available.

Blast

... Figure <xr id="fig:Agent_LifeCycle#1"/> illustrates the standard agent's life-cycle. ... Figure <xr id="fig:Agent_LifeCycle#2"/> illustrates the finer agent's life-cyle, ... <figure id="fig:Agent_Life_Cycle"> <twocolumns> <subfigure>

File:Standard Agent LifeCycle.png
Standard Agent's Life-Cycle

</subfigure> <break> <subfigure>

File:Finer Agent LifeCycle.png
Finer Agent's Life-Cycle

</subfigure> </twocolumns>

Life Cycles of Agent

</figure>

PSI-Blast

Iterations 2 2 10 10
E-value 0.002 10E-10 0.002 10E-10
Runtime
No. hits

Table 1: Different performances of PSI-Blast.


HHBlits

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