Difference between revisions of "Lab Journal - Task 4 (PAH)"
(→Evaluate sequence alignments) |
(→Explore structural alignments) |
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==Explore structural alignments== |
==Explore structural alignments== |
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| + | To explore different tools for building structural alignments the webservers themselves are used. For all tools the default parameters are kept.<br> |
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| − | ==Evaluate sequence alignments== |
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| + | As there are often more than one chain for the proteins we decided to take chain A for both our query 2pah and all different targets. |
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| − | The perl script hhmakemodel can be found in ''/usr/share/hhsuite/scripts''. It needs a input file in form of a result file from hhsearch with hit list and alignments (-i). |
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| + | '''SAP or CE'''<br> |
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| − | -d <pdbdirs> directories containing the pdb files (for PDB, SCOP, or DALI |
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| + | First, we wanted to do the structural alignment with the [http://mathbio.nimr.mrc.ac.uk/wiki/SAP SAP] webserver, but we did get an Error with this program. So we only used CE. Nevertheless, we tried SAP later again and this time it worked, but still we did not include it here. |
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| − | sequences) (default=/cluster/databases/pdb/all) |
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| − | -m <int> [<int> ...] pick hits with specified indices (default='-m 1') |
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| − | -ts <file.pdb> write the PDB-formatted models based on *pairwise* |
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| − | alignments into file.pdb |
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| + | ==Evaluate sequence alignments== |
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| − | So first a hhr file is crated with the FASTA file of our protein PAH and the pdb database. The output file is called hhsearch_PAH.hhr. Furthermore we set the maximal reported lines in summary and alignments to 10000:<br> |
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| + | The perl script hhmakemodel can be found in ''/usr/share/hhsuite/scripts''. It needs an input file in form of a result file from hhsearch with hit list and alignments (-i). |
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| + | |||
| + | So, first an hhr file was created with the FASTA file of our protein PAH and the pdb database. The output file was called hhsearch_PAH.hhr. Furthermore, we set the maximal reported lines in summary and alignments to 10000:<br> |
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<code> |
<code> |
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hhsearch -i /mnt/home/student/waldraffs/Masterpraktikum/PAH.fasta -d /mnt/project/pracstrucfunc13/data/hhblits/pdb70_current_hhm_db -o /mnt/home/student/waldraffs/Masterpraktikum/Task4/hhsearch_PAH.hhr -Z 10000 -B 10000 |
hhsearch -i /mnt/home/student/waldraffs/Masterpraktikum/PAH.fasta -d /mnt/project/pracstrucfunc13/data/hhblits/pdb70_current_hhm_db -o /mnt/home/student/waldraffs/Masterpraktikum/Task4/hhsearch_PAH.hhr -Z 10000 -B 10000 |
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</code> |
</code> |
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| − | 26 entries were found. Two of them |
+ | 26 entries were found. Two of them were also used in explore structural alignments: 1j8u, 3luy. |
| − | + | For hhmakemodel.pl we one time choose eight entries thereby trying to get the whole range of e-values and scores on default it would only take the first (-m): |
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No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM |
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM |
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1 1phz_A Protein (phenylalanine 100.0 7E-165 3E-169 1181.8 0.0 429 1-429 1-429 (429) |
1 1phz_A Protein (phenylalanine 100.0 7E-165 3E-169 1181.8 0.0 429 1-429 1-429 (429) |
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19 1wyp_A Calponin 1; CH domain, 29.4 15 0.00057 29.7 0.0 68 201-269 47-115 (136) |
19 1wyp_A Calponin 1; CH domain, 29.4 15 0.00057 29.7 0.0 68 201-269 47-115 (136) |
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26 1a6s_A GAG polyprotein; core p 20.6 29 0.0011 28.0 0.0 42 141-196 42-83 (87) |
26 1a6s_A GAG polyprotein; core p 20.6 29 0.0011 28.0 0.0 42 141-196 42-83 (87) |
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| + | The second time we choose all 26 pdbs. Additionally a database had to be chosen, which includes those pdb entries (-d) and finally the models are written in PDB-format to model_PAH.pdb (-ts):<br> |
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| + | <code> perl /usr/share/hhsuite/scripts/hhmakemodel.pl -i /mnt/home/student/waldraffs/Masterpraktikum/Task4/hhsearch_PAH.hhr -d /mnt/project/pracstrucfunc13/data/pdb/20120401/entries/* -m 1 2 6 7 9 12 19 26 -ts /mnt/home/student/waldraffs/Masterpraktikum/Task4/model_PAH.pdb </code> |
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| + | |||
| + | [[Category: Phenylketonuria 2013]] |
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Latest revision as of 09:50, 27 August 2013
Explore structural alignments
To explore different tools for building structural alignments the webservers themselves are used. For all tools the default parameters are kept.
As there are often more than one chain for the proteins we decided to take chain A for both our query 2pah and all different targets.
SAP or CE
First, we wanted to do the structural alignment with the SAP webserver, but we did get an Error with this program. So we only used CE. Nevertheless, we tried SAP later again and this time it worked, but still we did not include it here.
Evaluate sequence alignments
The perl script hhmakemodel can be found in /usr/share/hhsuite/scripts. It needs an input file in form of a result file from hhsearch with hit list and alignments (-i).
So, first an hhr file was created with the FASTA file of our protein PAH and the pdb database. The output file was called hhsearch_PAH.hhr. Furthermore, we set the maximal reported lines in summary and alignments to 10000:
hhsearch -i /mnt/home/student/waldraffs/Masterpraktikum/PAH.fasta -d /mnt/project/pracstrucfunc13/data/hhblits/pdb70_current_hhm_db -o /mnt/home/student/waldraffs/Masterpraktikum/Task4/hhsearch_PAH.hhr -Z 10000 -B 10000
26 entries were found. Two of them were also used in explore structural alignments: 1j8u, 3luy. For hhmakemodel.pl we one time choose eight entries thereby trying to get the whole range of e-values and scores on default it would only take the first (-m):
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 1phz_A Protein (phenylalanine 100.0 7E-165 3E-169 1181.8 0.0 429 1-429 1-429 (429) 2 1j8u_A Phenylalanine-4-hydroxy 100.0 3E-135 1E-139 951.9 0.0 325 103-427 1-325 (325) 6 2v27_A Phenylalanine hydroxyla 100.0 3.6E-74 1.4E-78 528.8 0.0 231 172-406 13-248 (275) 7 2qmx_A Prephenate dehydratase; 98.2 1.1E-09 4E-14 98.4 0.0 67 33-99 199-266 (283) 9 3luy_A Probable chorismate mut 98.1 3.3E-09 1.2E-13 97.7 0.0 67 33-99 206-274 (329) 12 1qey_A MNT-C, protein (regulat 54.0 3.4 0.00013 28.3 0.0 12 189-200 18-29 (31) 19 1wyp_A Calponin 1; CH domain, 29.4 15 0.00057 29.7 0.0 68 201-269 47-115 (136) 26 1a6s_A GAG polyprotein; core p 20.6 29 0.0011 28.0 0.0 42 141-196 42-83 (87)
The second time we choose all 26 pdbs. Additionally a database had to be chosen, which includes those pdb entries (-d) and finally the models are written in PDB-format to model_PAH.pdb (-ts):
perl /usr/share/hhsuite/scripts/hhmakemodel.pl -i /mnt/home/student/waldraffs/Masterpraktikum/Task4/hhsearch_PAH.hhr -d /mnt/project/pracstrucfunc13/data/pdb/20120401/entries/* -m 1 2 6 7 9 12 19 26 -ts /mnt/home/student/waldraffs/Masterpraktikum/Task4/model_PAH.pdb
