Difference between revisions of "Sequence Alignments TSD"
From Bioinformatikpedia
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| − | ''"We’re sorry. It’s not us. It’s the monster. The bank isn’t like a man."'' |
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| − | ''"Yes, but the bank is only made of men."'' |
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| − | ''"No, you’re wrong there—quite wrong there. The bank is something else than men. It happens that every man in a bank hates what the bank does, and yet the bank does it. The bank is something more than men, I tell you. It’s the monster. Men made it, but they can’t control it."'' |
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| − | Steinbeck - Grapes of Wrath |
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| − | == Test == |
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| − | I will ref in the text like so <xr id="fig:tsd_2gjx"/>. |
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| − | <figure id="fig:tsd_2gjx"> |
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| − | [[Image:TSD 2gjx ab.png|300px|thumb|<caption>'''Figure 2''': Shown is Hex A with the alpha subunit in red and beta subunit in blue. Figure has been rendered in pymol based on PDB entry [http://www.pdb.org/pdb/explore/explore.do?structureId=2gjx 2gjx]</caption>]] |
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| − | </figure> |
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== Sequence searches == |
== Sequence searches == |
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There are several alignment methods provided by various initiatives, who tackle the problem of sequence searches. |
There are several alignment methods provided by various initiatives, who tackle the problem of sequence searches. |
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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. |
+ | 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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Revision as of 19:11, 1 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.
