Difference between revisions of "Homology Modeling of ARS A"
From Bioinformatikpedia
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== HHpred == |
== HHpred == |
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The programs used for TASK 2 are heuristics, which produce local alignments. If we call modeller with only one template structure, we need to globally align the seqeunces. |
The programs used for TASK 2 are heuristics, which produce local alignments. If we call modeller with only one template structure, we need to globally align the seqeunces. |
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| − | To create pairwise alignments with the Needleman-Wunsch algorithm, we |
+ | To create pairwise alignments with the Needleman-Wunsch algorithm, we installed the European Molecular Biology Open Software (EMBOSS). |
<code> |
<code> |
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| + | sudo apt-get install emboss |
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| − | wget ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-latest.tar.gz <br> |
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| − | tar -xzf EMBOSS-latest.tar.gz <br> |
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| − | cd EMBOSS-6.3.1/ <br> |
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| − | ./configure <br> |
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| − | sudo make <br> |
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| − | sudo make install <br> |
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</code> |
</code> |
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Revision as of 13:45, 7 June 2011
HHpred
We used the webserver and
Modeller
Proteins used as templates
We identified the following proteins (see Alignment TASK) as potential targets for homology modeling:used the following
| SeqIdentifier | Seq Identity (from TASK 2) | source | Protein function | True homolog (HSSP) | Seq Identity (pairw. ali.) |
|---|---|---|---|---|---|
| 1P49 | 39.0% | Homo Sapiens | Steryl-Sulfatase | yes | ? |
| 1FSU | 28.0% | Homo Sapiens | Arylsulfatase B | yes | 26.5% |
| 2VQR | 20.0% | Rhizobium leguminosarum | Sulfatase | no | ? |
| 3ED4 | 32.0% | Escherichia coli | Arylsulfatase | yes | ? |
Our potential tmeplates, identified by the database searches contain all homologs with known structure, regarding to HSSP.
Pairwise alignments
The programs used for TASK 2 are heuristics, which produce local alignments. If we call modeller with only one template structure, we need to globally align the seqeunces. To create pairwise alignments with the Needleman-Wunsch algorithm, we installed the European Molecular Biology Open Software (EMBOSS).
sudo apt-get install emboss
