Difference between revisions of "Sequence Alignments TSD"
From Bioinformatikpedia
(→Blast: test) |
|||
| Line 3: | Line 3: | ||
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=== |
||
| − | <!-- <figure id="fig:tsd_gm2"> |
||
| − | [[Image:TSD GM2 ganglioside.png|300px|thumb|<caption>TODO</caption>]] |
||
| − | </figure> --> |
||
| − | |||
| − | ... |
||
| − | 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> |
||
| − | [[Image:Standard Agent LifeCycle.png|frame|<caption>Standard Agent's Life-Cycle</caption>]] |
||
| − | </subfigure> |
||
| − | <break> |
||
| − | <subfigure> |
||
| − | [[Image:Finer Agent LifeCycle.png|frame|<caption>Finer Agent's Life-Cycle</caption>]] |
||
| − | </subfigure> |
||
| − | </twocolumns> |
||
| − | <center><small><caption>Life Cycles of Agent</caption></small></center> |
||
| − | </figure> |
||
===PSI-Blast=== |
===PSI-Blast=== |
||
Revision as of 18:36, 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
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.
